Agenda packet — City Council and Concurrent Authorities, May 23, 2023 (part 6 of 8)

French Camp Slough and Duck Creek
Levees along Duck Creek are clear of trees and shrubs. Adjacent lands are largely agriculture with urban development beginning to extend into these lands. French Camp Slough upstream of the confluence with Duck Creek is very similar in character to Duck Creek. Construction of the new Duck Creek levee would result in impacts to 2 acres of riparian trees and shrubs and 2 acres of wetlands. Project construction and compliance with the Vegetation ETL would have a less than significant impact in these areas.

Levees along French Camp Slough would be improved through installation of a cutoff wall. This would require removal of 15.75 acres of woody riparian trees and shrubs, including approximately 5,500 lf of SRA habitat. This impact would be significant and unavoidable because there would be a permanent loss of riparian habitat, including SRA and loss of natural communities and wildlife habitat.

ALTERNATIVE 7B
Vegetation that could be removed as a result of project construction under Alternative 7b. Impacts on vegetation would be similar to those described for Alternative 7a except that Alternative 7b includes levee improvements and new levee segments in RD 17. Overall, the following vegetation could be removed or directly affected by implementation of Alternative 7b: 49,586 lf of SRA, 92 acres of waterside trees and shrubs, 135 acres of landside trees and shrubs and 15 acres of wetlands.

All woody riparian vegetation not removed for construction of the structural FRM features would be removed to achieve compliance with the Vegetation ETL, with the exception of approximately 25 percent of the waterside vegetation, which is assumed to be allowed to remain under a vegetation variance. The levee slopes and 15 to 20 feet landward of the levee would be permanently maintained free of trees and shrubs. Once construction is complete, the landside levees and easements would be maintained free of woody vegetation. This impact is significant and unavoidable because it would eliminate, in perpetuity, nearly all remaining landside trees and shrubs throughout the project footprint. Details of impacts by location for Alternative 7b are provided below.

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San Joaquin County, CA Affected Environment and Environmental Consequences North Stockton
(Mosher Slough, Tenmile Slough, Fivemile Slough, Fourteenmile Slough) Under Alternative 7b, the levee improvements and gates proposed along with their impacts are the same as those proposed under Alternative 7a. The impacts would be significant and unavoidable because there would be a permanent loss of riparian habitat, including wetlands and loss of natural communities and wildlife habitat.

Central Stockton
(Calaveras River, Smith Canal, Stockton Diverting Canal, SJR upstream of the Calaveras River to French Camp Slough and Duck Creek)
Under Alternative 7b, the levee improvements and gates proposed are the same as those proposed under Alternative 7a, except that Alternative 7b does not include construction of a new levee extension on Duck Creek. Nevertheless, Alternative 7b would result in significant and unavoidable impacts to vegetation because they represent a permanent loss of riparian habitat, including SRA and wetlands and loss of natural communities and wildlife habitat.

RD 17
French Camp Slough
Like the northern French Camp Slough levees that are part of Central Stockton, the southern levees would be improved through installation of a cutoff wall. Construction would require removal of SRA, waterside and landside trees and shrubs and wetlands. This impact would be significant and unavoidable because there would be a permanent loss of riparian habitat, including SRA and wetlands and loss of natural communities and wildlife habitat.

SJR
Levee improvements along the SJR include construction of cutoff walls, levee slope reshaping, restoration of levee heights where needed, construction of new levee segments construction of landside seepage berms and erosion protection. Construction would require removal of SRA, waterside and landside trees and shrubs and wetlands throughout the entire project footprint. This impact would be significant and unavoidable because there would be a permanent loss of riparian habitat, including SRA and wetlands and loss of natural communities and wildlife habitat.

ALTERNATIVE 8A
Under Alternative 8a, the effects would be similar to that described for Alternative 7a, except that the impacts would extend further upstream on the Lower Calaveras River and on the southwestern levee of the Stockton Diverting Canal. Overall, the following vegetation could be removed or directly affected by implementation of Alternative 8a: 25,674 lf of SRA, 37 acres of waterside trees and shrubs, 123 acres of landside trees and shrubs and 11 acres of wetlands.

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San Joaquin County, CA Affected Environment and Environmental Consequences North Stockton
(Mosher Slough, Tenmile Slough, Fivemile Slough, Fourteenmile Slough) Alternative 8a includes the same flood system improvements and vegetation impacts as are described for Alternative 7a. Therefore impacts to vegetation would be significant and unavoidable because there would be a permanent loss of riparian habitat and wetlands and loss of natural communities and wildlife habitat.

Central Stockton
(Calaveras River, Smith Canal, Stockton Diverting Canal, SJR upstream of the Calaveras River to French Camp Slough and Duck Creek)
Alternative 8a includes the same flood system improvements and vegetation impacts as are described for Alternative 7a, except that additional levee improvements would occur on Calaveras River and on the Stockton Diverting Canal. Some wetlands would be affected, but there are few trees and shrubs on the Stockton Diverting Canal or the additional reaches of the Calaveras River. Impacts to vegetation on the Calaveras River, Smith Canal and the SJR upstream of the Calaveras River to French Camp Slough would be significant and unavoidable because there would be a permanent loss of riparian habitat, including SRA and wetlands and loss of natural communities and wildlife habitat.

Stockton Diverting Canal and Duck Creek
Levees along the Stockton Diverting Canal would be improved through installation of a cutoff wall.

Construction would require removal of all vegetation on the upper half of the levee slopes. Further, Duck Creek is clear of woody vegetation. Most of these levees are maintained clear of woody vegetation. There are just a few scattered trees that would be removed during construction on the levee slopes along the Stockton Diverting Canal. This impact would be less than significant.

ALTERNATIVE 8B
Overall, the following vegetation could be removed or directly affected by implementation of Alternative 8b: 51,985 lf of SRA, 92 acres of waterside trees and shrubs, 153 acres of landside trees and shrubs and 15 acres of wetlands. This impact would be significant because it represents a substantial adverse effect on riparian habitat, including SRA and wetlands and loss of natural communities and wildlife habitat.

North Stockton
(Mosher Slough, Tenmile Slough, Fivemile Slough, Fourteenmile Slough) Alternative 8b includes the same flood system improvements and vegetation impacts as are described for Alternative 7a. Therefore impacts to vegetation would be significant and unavoidable because there would be a permanent loss of riparian habitat and wetlands and loss of natural communities and wildlife habitat.

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San Joaquin County, CA Affected Environment and Environmental Consequences Central Stockton
(Calaveras River, Smith Canal, Stockton Diverting Canal, SJR upstream of the Calaveras River to French Camp Slough and Duck Creek)
Alternative 8b includes the same flood system improvements and vegetation impacts as are described for Alternative 7a, except that additional levee improvements would occur on Calaveras River and on the Stockton Diverting Canal. Some wetlands would be affected, but there are few trees and shrubs on the Stockton Diverting Canal or the additional reaches of the Calaveras River. Impacts to vegetation on the Calaveras River, Smith Canal and the SJR upstream of the Calaveras River to French Camp Slough would be significant and unavoidable because there would be a permanent loss of riparian habitat, including SRA and wetlands and loss of natural communities and wildlife habitat.

Stockton Diverting Canal and Duck Creek
Levees along the Stockton Diverting Canal would be improved through installation of a cutoff wall.

RD 17
Alternative 8b includes the same flood system improvements and vegetation impacts in RD 17 as Alternative 7b that would be significant and unavoidable because there would be a permanent loss of riparian habitat, including SRA and wetlands and loss of natural communities and wildlife habitat.

ALTERNATIVE 9A
Overall, the following vegetation could be removed or directly affected by implementation of Alternative 9a: 25,508 lf of SRA, 37 acres of waterside trees and shrubs, 115 acres of landside trees and shrubs and 11 acres of wetlands. This impact would be significant because it represents a substantial adverse effect on riparian habitat, including SRA and wetlands and loss of natural communities and wildlife habitat.

North Stockton
(Mosher Slough, Tenmile Slough, Fivemile Slough, Fourteenmile Slough) Alternative 9a includes the same flood system improvements and vegetation impacts as Alternative 7a.

Therefore, impacts to vegetation would be significant and unavoidable because there would be a permanent loss of riparian habitat and wetlands and loss of natural communities and wildlife habitat.

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San Joaquin County, CA Affected Environment and Environmental Consequences Central Stockton
(Calaveras River, Smith Canal, Old Mormon Slough, SJR upstream of the Calaveras River to French Camp Slough and Duck Creek)
Alternative 9a proposes the same flood system improvements and would result in the same vegetation impacts as Alternative 7a, except that there would be construction of a diversion structure at the confluence of Old Mormon Slough with the Stockton Diverting Canal and excavation within Old Mormon Slough in order to establish the channel as a flood bypass (Mormon Channel Bypass). Impacts to vegetation would be significant and unavoidable because there would be a permanent loss of riparian habitat, including SRA and wetlands and loss of natural communities and wildlife habitat.

Mormon Channel Bypass
A diversion structure would be constructed in the left bank of the SDC and floodflows (1,200 cfs every 2 years) would be reintroduced to Old Mormon Slough below its confluence with the SDC. Channel improvements and improvements to existing roads and other infrastructure would require removal of a large number of trees and shrubs. Reintroducing flood flows to Old Mormon Slough by establishing the Mormon Channel Bypass would improve conditions for the remaining vegetation and would likely increase the health and encourage expansion of riparian vegetation along much of this channel. This impact would be significant and unavoidable because there would be a permanent loss of riparian habitat, including SRA and wetlands and loss of natural communities and wildlife habitat.

ALTERNATIVE 9B
Overall, the following vegetation could be removed or directly affected by implementation of Alternative 9b: 51,819 lf of SRA, 92 acres of waterside trees and shrubs, 135 acres of landside trees and shrubs and 15 acres of wetlands. This impact would be significant and unavoidable because there would be a permanent loss of riparian habitat, including SRA and wetlands and loss of natural communities and wildlife habitat.

North Stockton
(Mosher Slough, Tenmile Slough, Fivemile Slough, Fourteenmile Slough) Alternative 9b includes the same flood system improvements and vegetation impacts as Alternative 7a.

Therefore, impacts to vegetation would be significant and unavoidable because there would be a permanent loss of riparian habitat wetlands and loss of natural communities and wildlife habitat.

Central Stockton
(Calaveras River, Smith Canal, Old Mormon Slough, SJR upstream of the Calaveras River to French Camp Slough and Duck Creek)
Alternative 9b proposes the same flood system improvements and would result in the same vegetation impacts, as Alternative 7a, except that there would be construction of a diversion structure at the confluence of Old Mormon Slough with the Stockton Diverting Canal and excavation within Old Mormon Slough in order to establish the channel as a flood bypass (Mormon Channel Bypass). Impacts to vegetation would ATTACHMENT D 1248
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San Joaquin County, CA Affected Environment and Environmental Consequences be significant and unavoidable because there would be a permanent loss of riparian habitat, including SRA and wetlands and loss of natural communities and wildlife habitat.

Mormon Channel Bypass
A diversion structure would be constructed in the left bank of the SDC and floodflows (1,200 cfs every 2 years) would be reintroduced to Old Mormon Slough below its confluence with the SDC. Channel and existing road improvements and other infrastructure would require removal of a large number of trees and shrubs. Reintroducing flood flows to Old Mormon Slough and establishing the Mormon Channel Bypass would improve conditions for the remaining vegetation and would likely increase the health and encourage expansion of riparian vegetation along much of this channel. This impact would be significant and unavoidable because there would be a permanent loss of riparian habitat, including SRA and wetlands and loss of natural communities and wildlife habitat.

RD 17
Alternative 9b includes the same flood system improvements and vegetation impacts in RD 17 as Alternative 7b. These impacts would be significant and unavoidable because there would be a permanent loss of riparian habitat, including SRA and wetlands and loss of natural communities and wildlife habitat.

MITIGATION
Mitigation includes avoidance, minimization, remediation and compensation. Because construction would include establishment of compliance with the Vegetation ETL and also VFZ landside O&M easements, impacts to vegetation in the project footprint cannot be avoided, minimized or fully remediated.

Compensatory mitigation would be used to mitigate for project impacts. Even with mitigation, implementation of Alternatives 7a, 7b, 8a, 8b, 9a and 9b would remain substantial and would result in permanent, significant and unavoidable impacts.

Avoid and Minimize
During the design refinement phase, plans would be evaluated to reduce the impact on vegetation to the extent practicable. Refinements could include reduction in the project footprint. USACE will also seek a vegetation variance in order to comply with the Vegetation ETL. Reciept of a variance would allow vegetation to remain on the lower two thirds of the waterside levee slope and within the waterside easement.

In addition, if a variance is granted, USACE will seek opportunities to plant vegetation on the waterside of the levees in order to compensate for impacts to SRA habitat in accordance with the terms and conditions of the NMFS BO. The avoidance and minimization measures identified would be used to mitigate potential impacts to vegetation outside of the project footprint.

Install Exclusion Fencing along the Construction Work Area Perimeter and Implement General Measures to Avoid Effects on Sensitive Natural Communities and Special-Status Species To clearly demarcate the project boundary and protect sensitive natural communities, temporary exclusion fencing would be installed around the project boundaries (including access roads, staging areas, etc.) 1 week prior to the start of construction activities. The temporary fencing would be continuously maintained until all construction activities were completed so that construction equipment would be confined to the designated work areas, including any off site mitigation areas and access thereto. The exclusion fencing would be removed only after construction for the year is entirely completed.

Exclusionary construction fencing and explanatory signage would be placed around the perimeter of sensitive vegetation communities that could be affected by construction activities throughout the period ATTACHMENT D 1249
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San Joaquin County, CA Affected Environment and Environmental Consequences during which such effects occur. Signage would explain the nature of the sensitive resource and warn that no effect on the community is allowed. Where feasible, the fencing would include a buffer zone of at least 20 feet between the resource and construction activities. All exclusionary fencing would be maintained in good condition throughout the construction period.

Conduct Mandatory Contractor/Worker Awareness Training for Construction Personnel Before initiating any work in the project area, including grading, a qualified biologist would conduct mandatory contractor/worker awareness training for all construction personnel. It would be provided to brief them on the need to avoid effects on sensitive biological resources (e.g., riparian habitat, special-status species, wetlands and other sensitive biological communities) and the penalties for not complying with permit requirements. The biologist would inform all construction personnel about the life history of specialstatus species with potential for occurrence on the site, the importance of maintaining habitat and the terms and conditions of the BO or other authorizing document. Proof of this instruction would be submitted to USFWS and CDFW.

The training would also cover the restrictions and guidelines that must be followed by all construction personnel to reduce or avoid effects on sensitive biological communities and special-status species during project construction. The crew leader would be responsible for ensuring that crew members adhere to the guidelines and restrictions. Educational training would be conducted for new personnel as they are brought on the job. General restrictions and guidelines for vegetation and wildlife that must be followed by construction personnel are listed.
 Project-related vehicles would observe the posted speed limit on hard-surfaced roads and a 10- mile-per-hour speed limit on unpaved roads during travel in the project site.  Project-related vehicles and construction equipment would restrict off-road travel to the designated construction area.
 To prevent possible resource damage from hazardous materials such as motor oil or gasoline, construction personnel would not service vehicles or construction equipment outside designated staging areas.

Retain a Biological Monitor
A qualified biologist would monitor construction activities adjacent to sensitive biological resources (e.g., special-status species, riparian habitat, wetlands, elderberry shrubs), as needed. The biologists would assist the construction crew, as needed, to comply with all project implementation restrictions and guidelines. In addition, the biologist would be responsible for ensuring that construction barriers fencing is maintained adjacent to sensitive biological resources.

Remediation
After construction, structural FRM features and easement areas would be reseeded with native grasses and herbs and/or planted with appropriate herbaceous riparian and wetland species.

Compensation
Vegetation impacts that cannot be mitigated through avoidance, minimization or remediation will be mitigated through compensation. A 14 acre mitigation site has been identified at the setback area in the Delta Front portion of the study area. This site would be planted with primarily VELB compensation (as discussed in Section 5.12) and associated riparian habitat. Additional compensation required for riparian, SRA, wetland and open water habitats would be accomplished through the purchase of credits at a ATTACHMENT D 1250
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San Joaquin County, CA Affected Environment and Environmental Consequences mitigation bank. More information regarding proposed compensation can be found in the Habitat Mitigation, Monitoring and Adaptive Management Plan (Environmental Addendum).

Where possible, on site mitigation areas would be the preferred action. USACE would seek opportunities to increase on site mitigation options during the design phase of the project, in accordance with the terms and conditions of the NMFS BO. Mitigation site selection would avoid areas where future disturbance or maintenance is likely. A revegetation plan would be prepared by a qualified biologist or landscape architect and reviewed by the appropriate agencies. The revegetation plan would specify the planting stock appropriate for each riparian cover type and each mitigation site, ensuring the use of genetic stock from the project area and would employ the most successful techniques available at the time of planting.

The plantings would be maintained and monitored, as necessary, for 3 to 5 years, including weed removal, irrigation and herbivory protection. USACE would submit annual monitoring reports of survival to the regulatory agencies including USFWS, NMFS and CDFW. Replanting would be necessary if success criteria are not met and replacement plants would subsequently be monitored and maintained to meet the success criteria. The mitigation would be considered successful when the plants meet the success criteria, the vegetation no longer requires active management and is arranged in groups that, when mature, replicate the area, natural structure and species composition of similar plant communities in the region.

WILDLIFE
This section describes the affected environment and environmental consequences relating to wildlife for the LSJR project. The significance of the impacts and mitigation measures to reduce impacts are also discussed. Note that special status wildlife species are discussed in Section 5.12, SPECIAL STATUS SPECIES.

ENVIRONMENTAL SETTING
Regulatory Framework
The laws, regulations and requirements that apply to wildlife are listed below and summarized in Chapter 7, Compliance with Applicable Laws, Policies and Plans.

Federal
 EO 13112 (Invasive Species)
 FWCA of 1934, as amended
 Migratory Bird Treaty Act of 1918
State
• CFGC
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San Joaquin County, CA Affected Environment and Environmental Consequences Local
 California Aquatic Invasive Species Management Plan, January 2008  City of Lathrop General Plan (Polices 1, 2 and 7)
 San Joaquin County General Plan (Objective 1 and 2, Policies 1, 4, 5,6 and 8)  San Joaquin County Multi-Species Habitat Conservation and Open Space Plan San Joaquin County Titles 9-1505 and 9-1510)
 Stockton General Plan 2035 (NCR-1 and NCR-2)
Existing Conditions
The project area is situated at an ecological crossroads between the habitats of the San Francisco Estuary and the riverine habitats of the San Joaquin Valley floor and the uplands from which SJR and tributaries flow. The project area extends from riverine areas along the lower SJR mainstem and its tributaries into the southeast portion of the Delta. Much of the project area is highly urbanized with urban development surrounded by agricultural lands that are primarily orchards, vineyards and row or field crops. Rice is also farmed in portions of the project area within the Delta. Upstream, State and Federal conservation lands provide habitat for a wider diversity of wildlife. The Caswell Memorial State Park is located near Manteca in San Joaquin County. The SJR National Wildlife Refuge is upstream along the mainstem of the SJR.

Terrestrial wildlife in the north and central Stockton area is comprised mainly of those species well-adapted to surviving at the urban-agriculture interface. In RD 17, the agricultural lands in the project area are more extensive. Common wildlife species are those typically associated with agriculture (alfalfa, row crops and orchard) and ruderal habitat (AECOM, 2011:3.6-14). Some larger stands of riparian forest in RD 17 provide habitat for a greater diversity of wildlife, including the Federally- protected Riparian Brush Rabbit. This species and other special status species are discussed in Section 5.12.

Efforts are underway through the Delta Stewardship Council’s Delta Plan and the Bay Delta Conservation Plan, to conserve and restore extensive acres of habitat for fish and wildlife throughout the Delta, including near the project area.

Wildlife that are known or could reasonably be expected to occupy habitat in the project area are described below. The information in this section is drawn from AECOM (2011) and direct observations during reconnaissance visits.

Riparian Habitats
Riparian habitats are considered to be among the most productive and diverse wildlife habitats in California.

Riparian habitats provide important nesting, resting and foraging for resident and migratory birds. They also provide critical ecological function as wildlife movement corridors. Riparian habitat is designated by CDFW as sensitive natural and provides high value to wildlife (ICF, 2013).

Species commonly found in Central Valley riparian habitat include: acorn woodpecker, black phoebe, Bullock’s oriole, house wren, oak titmouse, western kingbird, western scrub-jay, yellow-rumped warbler and white egrets. Overstory trees may provide roost sites for tree-associated bat species and nest sites for raptors, such as Swainson’s hawk (discussed further in Section 5.12), red-tailed hawk, white-tailed kite, red-shouldered hawk and great horned owl, as well as for l as herons and egrets. Overstory trees also provide suitable habitat for songbirds such as Bullock’s oriole, yellow-rumped warbler, tree swallow and western scrub jay. Understory habitat provides cover for rodents, raccoons, opossum and striped skunk. Groundnesting birds such as spotted towhee may forage among the vegetation and leaf litter. A few large patches of riparian forest with dense understory shrub layers are known to support riparian brush rabbit, which is ATTACHMENT D 1252
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San Joaquin County, CA Affected Environment and Environmental Consequences Federally-listed and State-listed as endangered (ICF, 2013; AECOM, 2011). Riparian habitats also provide cover and foraging habitat for reptiles and amphibians, such as terrestrial garter snake, gopher snake, Pacific tree frog and western toad.

Agricultural Lands
Agricultural lands in the project area include orchards, vineyards, row and field crops, alfalfa fields and rice. Ruderal species grow along the edges of fields and irrigation ditches, some of which contain water and associated aquatic plants. Row and field agricultural lands can provide high value foraging habitat for numerous resident and wintering raptors, songbirds, shorebirds and wading birds. Agricultural lands also provide foraging habitat for rodents, including deer mouse and California meadow vole; other mammals including coyote, raccoon, Virginia opossum; and reptiles, including gopher snake and terrestrial garter snake (ICF, 2013).

Orchard crops typically provide less value to wildlife but may be used for nesting or foraging by redshouldered hawk, American crow, yellow-billed magpie, brown-headed cowbird, European starling, mourning dove and rock dove (ICF, 2013). Wildlife in agricultural ditches is typically limited because of the regular disturbance associated with maintenance activities and the absence of adjacent natural upland vegetation. Agricultural ditches, however, can support marsh-associated species, including birds such as marsh wren, sparrow species, white egret and mallard duck; amphibians such as Pacific chorus frog and bullfrog; and reptiles such as western pond turtle, which is a California species of special concern (Section

5.12).

Nonnative Annual Grasslands and Ruderal Lands
Grasslands in the project area are dominated by nonnative annual grasses and ruderal vegetation and may support stands of noxious weeds. Grassland generally occurs in disturbed areas, such as levee faces and edges of agricultural fields and roads. The annual grasslands in the project area contain a relatively large proportion of ruderal species, likely because of substantial disturbance from human activities.

Annual grasslands provide nesting and foraging habitat for several species of songbirds, including savanna sparrow, white-crowned sparrow and western meadowlark; and foraging habitat for several species of raptors, including red-tailed hawk and great-horned owl. Reptiles found in these habitats include California kingsnake, gopher snake and western rattlesnake. California ground squirrels commonly occur in annual grassland habitat (ICF, 2013).

Annual grasslands provide foraging habitat for numerous bat species and foraging and denning habitat for the American badger. Bird species for which annual grassland provides primary foraging and nesting habitat include northern harrier and western burrowing owl. Annual grassland also provides foraging habitat for raptor species, including Swainson’s hawk and white-tailed kite. These grasslands also serve as primary foraging habitat for loggerhead shrike, grasshopper sparrow, purple martin, tricolored blackbird and yellowheaded blackbird. Ground squirrel burrows provide important nesting habitat for western burrowing owls.

Additionally, annual grassland areas surrounding levees and those adjacent to aquatic habitat may provide potential winter hibernacula for the giant garter snake (GGS).

Developed Lands
Developed lands include levee roads and crowns, roads, railways, buildings and landscaped areas as well as areas that are disturbed and are not vegetated. These areas support relatively low wildlife diversity.

Wildlife found in these areas are adapted to human disturbance and altered environments. These areas likely support common wildlife species, including house sparrow, house finch, European starling, American crow, mourning dove, raccoon, opossum, California ground squirrel and California meadow vole, to name a few.

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San Joaquin County, CA Affected Environment and Environmental Consequences Scattered landscape trees and shrubs associated with this area may provide nesting habitat for the abovelisted common birds. Barren habitats provide primary habitat for the western burrowing owl, a specialstatus wildlife species that is discussed further in Section 5.12.

Open Water Areas
Open water in the project area includes the SJR, Fourteenmile Slough, Fivemile Slough, Tenmile Slough, Smith Canal, French Camp Slough (perennial drainages), agricultural ditches (ditches) and small artificial ponds (ponds). Open water provides breeding, foraging and migration habitat for numerous wildlife species.

Mammal species commonly known to use perennial aquatic open water habitats include river otter, which uses these areas for foraging and escape cover and muskrat, which may use deepwater areas as migration corridors between suitable foraging areas. Open water areas also provide essential foraging habitat for wading birds, including great blue heron, great egret and snowy egret; numerous waterfowl species, including mallard, ruddy duck and bufflehead; other water birds, including eared grebe, double-crested cormorants and American white pelicans; and land birds, including black phoebe and belted kingfisher.

These areas also provide rearing habitat, escape cover and foraging habitat for reptiles and amphibians, including common garter snake), bullfrog, Pacific tree frog and western toad. The vegetated areas below the ordinary high water mark provide nesting habitat for numerous songbirds, including red-winged blackbird and marsh wren and wading birds such as Virginia rail.

Emergent Wetlands
Emergent wetland vegetation occurs in agricultural ditches throughout the project area and along the margins of some parts of the SJR and its tributaries and associated sloughs. Emergent wetland provides important wildlife habitat value including nesting and foraging habitat for several songbirds, including redwinged blackbird and marsh wren; foraging and nesting habitat for Virginia rail; and foraging and cover habitat for the reptiles and amphibians mentioned above for open water.

Invasive Species
Invasive species are plants, animals or microbes that are not native to an environment and once introduced, establish, quickly reproduce and spread and cause harm to the environment, economy and/or human health.

Invasive species threaten the diversity or abundance of native species through competition for resources, predation, parasitism, interbreeding with native populations, transmitting diseases or causing physical or chemical changes to the invaded habitat (CDFW, 2014). Both terrestrial and aquatic invasive species are potentially present in the project area. The American bullfrog and house sparrows are known to occur in the project area.

ASSESSMENT METHODS AND BASIS OF SIGNIFICANCE
Assessment Methods
This evaluation of wildlife is based on professional standards and information cited throughout the section.

The key effects were identified and evaluated based on the environmental characteristics of the LSJR project area and the magnitude, intensity and duration of activities related to the construction and operation of this project.

Direct and indirect effects on wildlife species were quantitatively and qualitatively evaluated based on the potential for species occurrence in habitat located in the project area. Note that special status species are addressed in Section 5.12. Habitat was determined based upon a literature review, a two-day reconnaissance site visit and Google Earth. The project footprint was imported into Google Earth and vegetation cover was ATTACHMENT D 1254
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San Joaquin County, CA Affected Environment and Environmental Consequences identified and mapped. Acreages of direct effects were calculated for each alternative and are presented in separate tables. The analysis of potential indirect effects on wildlife is qualitative in nature (i.e., noise disturbance, dust accumulation) and was determined based on the proximity of project activities to know species locations or potential habitat. For wildlife movement, existing and accessible drainage corridors were qualitatively assessed with respect to their relative function to facilitate wildlife movement through the landscape.

Effect Assumptions
Assumptions regarding project effects on vegetation and wetlands (wildlife habitat) are discussed in Section

5.9, VEGETATION and Section 5.7, WETLANDS AND OTHER WATERS OF THE UNITED STATES.

For wildlife, this additional assumption is made: Loss of agricultural and annual grassland vegetation would not be considered an adverse effect from a wildlife standpoint if the habitats are being converted to a higher value native habitat or to an equivalent value habitat. Because these habitats are common and not considered sensitive community types, the impacts may not be significant.

Effect Mechanisms
Wildlife resources could be directly and indirectly affected by and operation of the project alternatives. The following types of activities could cause varying degrees of effects on these resources.

Construction-Related Effects
 Vegetation removal for construction of levee improvements and other project features.  Grading and fill placement during construction of levee alternatives.  Channel dewatering or installation of temporary water-diversion structures.  Temporary stockpiling and side-casting of soil, construction materials or other construction wastes.  Short-term construction-related noise (from equipment).  Soil compaction, dust and runoff.
 Runoff of herbicides, fertilizers, diesel fuel, gasoline, oil, raw concrete or other toxic materials used for levee construction, O&M into sensitive biological resource areas (e.g., riparian habitat, wetlands).
 Placement of rock slope protection on the landside of levees.

Post-Construction Effects
 O&M activities, including removal of weeds, shrubs and trees up to four times per year and reconditioning of levee slopes and road, as needed.
 Altering of hydrology.
 Toxicity associated with herbicides, insecticides and rodenticides.  Increase habitat for native competitors or predators.  Introduction of invasive nonnative species.

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San Joaquin County, CA Affected Environment and Environmental Consequences Basis of Significance
For this analysis, an environmental effect was considered potentially significant related to wildlife if it would result in any of the effects listed below. These effects are based on NEPA standards, State CEQA Guidelines Appendix G (14 CCR 15000 et seq.) and standards of professional practice.  Substantial loss, degradation or fragmentation of any natural communities or wildlife habitat.  Substantial interference with the movement of any native resident or migratory wildlife species or with established native resident or migratory wildlife corridors or impedance of the use of native wildlife nursery sites.
 Contribution to a substantial reduction or elimination of species diversity or abundance.  Substantial effects on any riparian habitat or other sensitive natural community identified in local or regional plans, policies or regulations or by NMFS, USFWS or CDFW.  Conflict with the Central Valley Flood Protection Plan (2012).  Conflict with the provisions of the San Joaquin County Multi-species Conservation and Open Space Plan (2000).
 Conflict with the San Joaquin County General Plan, City of Stockton General Plan, Lathrop General Plan or the Manteca General Plan.

ALTERNATIVE 1 - NO ACTION
Under the No Action Alternative, USACE would not participate in construction of the proposed project.

There would be no construction-related affects to wildlife. However, the flood risk in the project area would remain elevated and flood fighting activities could be required. Wildlife habitats could be degraded or reduced due to erosion and flooding and wildlife swept away in the flood waters. The magnitude of the impacts would depend upon the location of the levee breach, severity of the storm and river flows at the time of flooding. Predicting these events and providing a determination of significance is not possible based on the information available at this time. Therefore, identification of potential effects is too speculative for meaningful consideration.

ALTERNATIVE 7A
Because vegetation cover is a general indicator of terrestrial habitat, the potential impacts to vegetation described in Section 5.9 provide a measure of impacts to wildlife. Vegetation would be removed from the construction footprint at the time each reach is constructed.

Potential impacts to wildlife would be similar throughout the project area. North and central Stockton and the northern and southern portions of RD 17 are developed urban areas adjacent to agricultural lands.

Because this area is very urbanized, the primary effects to wildlife would be to avian species. Trees in the project area, including riparian trees on and adjacent to the levees, provide nesting habitat for many avian species in the area. Construction would likely occur from May through October when birds commonly nest in the area. These disturbances could cause nest abandonment and subsequent loss of eggs or developing young in the project area. All migratory birds and raptors are protected under the Migratory Bird Treaty Act (MBTA) and CFWC Sections 3503 and 3503.5.

Although urban lands do not provide high value wildlife habitat, some species are found in and adjacent to these areas. Common wildlife at the urban-agriculture interface includes birds, raccoons, possums, skunks and squirrels. Where riparian vegetation abuts agricultural lands, raptors may be common, along with jack rabbits and occasionally coyotes. Project construction and long-term O&M would result in significant short- and long-term affects to these species.

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San Joaquin County, CA Affected Environment and Environmental Consequences Short-term significant impacts to birds and other wildlife could be experienced in areas adjacent to the construction footprint but within the impact area for noise, vibration and dust. Potential conversion of agricultural land as a result of the proposed project would reduce foraging habitat for migratory birds. The proposed project would have short- and long-term impacts on resident and migratory birds because of the loss of nesting, resting and foraging habitat and impacts to commonly occurring wildlife. This is based upon the loss of migratory and movement corridors that would result from vegetation removal required for construction of structural flood risk reduction features, Vegetation ETL VFZ and maintenance of the O&M easement. Mitigation measures to avoid and minimize short-term construction impacts are described below.

Compensatory mitigation measures to off-set impacts to habitat are described in Section 5.9, VEGETATION. Although mitigation would reduce short- and long-term impacts to wildlife, impacts would remain significant and unavoidable.

ALTERNATIVE 7B
Implementing Alternative 7b would result in impacts that are similar in type to, but greater in extent than, those described under Alternative 7a. This is because Alternative 7b includes the same features in north and central Stockton as for Alternative 7a, but also extents south to include northern, western and southern levees around RD 17. For the same reasons as described under Alternative 7a, short- and long-term impacts to wildlife would be significant and unavoidable, even when considering mitigation to avoid, minimize, rectify and compensate for impacts.

ALTERNATIVE 8A
Implementing Alternative 8a would result in impacts that are similar in type to, but greater in extent than, Alternative 7a. This is because Alternative 8a includes the same features as Alternative 7a, but also includes additional levee improvements on the Lower Calaveras River and along the Stockton Diverting Canal. For the same reasons as described under Alternative 7a, short- and long-term impacts to wildlife from implementing Alternative 8a would be significant and unavoidable, even with mitigation to avoid, minimize, rectify and compensate for impacts.

ALTERNATIVE 8B
Implementing Alternative 8b would result in impacts that are similar in type to, but greater in extent than, to those in Alternative 7b. This is because Alternative 8b includes the same features as Alternative 7b, but also includes additional levee improvements on the Lower Calaveras River and along the Stockton Diverting Canal. Like Alternative 7b, Alternative 8b includes levee improvements along northern, western and southern levees in RD 17. For the same reasons as described under Alternative 7a, short- and long-term impacts to wildlife from implementing Alternative 8b would be significant and unavoidable, even with mitigation to avoid, minimize rectify and compensate for impacts.

ALTERNATIVE 9A
Impacts to wildlife from implementing Alternative 9a would be the same as those described for Alternative 7a, except for the inclusion of channel excavation and related work required to restore flood flows to Old Mormon Slough. For the same reasons as described under Alternative 7a, short- and long-term impacts to wildlife from implementing Alternative 9a would be significant and unavoidable, even with mitigation to avoid, minimize, rectify and compensate for impacts.

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San Joaquin County, CA Affected Environment and Environmental Consequences ALTERNATIVE 9B
Impacts to wildlife from implementing Alternative 9b would be similar in type and extent to Alternative 7b. For the same reasons as described under Alternative 7a, short- and long-term impacts to wildlife from implementing Alternative 9b would be significant and unavoidable, for the same reasons as described under Alternative 7a, even with mitigation to avoid, minimize, rectify and compensate for impacts.

MITIGATION
The same mitigation measures apply to all of the action alternatives, although the amount of compensatory mitigation would vary based upon the amount and quality of habitat temporarily and permanently affected by the project. Measures to avoid potential impacts to special status species are described in Section 5.12 and would also benefit more common wildlife. Mitigation described in Section 5.9, VEGETATION, would also avoid, minimize, rectify and/or compensate for potential impacts to wildlife. If a vegetation variance was approved and some compensatory mitigation was accomplished on site, then short- and long-term impacts to wildlife habitat would be greatly reduced. However, because new plantings would take many years to establish, a temporal loss would remain. In addition, even with a vegetation variance, some areas that currently support trees and shrubs would be maintained permanently in herbaceous vegetation after construction. For these reasons, even if a vegetation variance were approved, impacts to wildlife would remain significant and unavoidable.

FISHERIES
This section describes the affected environment and environmental consequences to fisheries for the LSJR project. The significance of the impacts and mitigation measures to reduce impacts are also discussed.

ENVIRONMENTAL SETTING
Regulatory Framework
The following Federal and State laws and regulations apply to the resources covered in this chapter.

Descriptions of the laws and regulations can be found in Chapter 7.

Federal
 CWA
 ESAMagnuson-Stevens Fishery Conservation and Management Act State
 California ESA
 CFGC Section 1600: Streambed Alteration Agreements
Existing Conditions
North Stockton
The North Stockton sloughs provide fish spawning, rearing and/or migratory habitat for a diverse number of native, nonnative and special status species (Table 5-34). Many of the nonnative resident fish species are more tolerant of warm water, low dissolved oxygen and disturbed environments than native species as encountered in the North Stockton area during most of the year. In general, they are adapted to warm, slowmoving and nutrient-rich waters (Moyle, 2002).

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San Joaquin County, CA Affected Environment and Environmental Consequences Table 5-34: Fish Species Reported in the Study Area
Native Species Introduced Species
hitch Lavinia exilicauda American shad Alosa sapidissima Blackfish Orthodon microlepidotus threadfin shad Dorosoma petenense San Joaquin roach Lavinia symmetricus sp. goldfish Carassius auratus Hardhead Mylopharodon conocephalus red shiner Cyprinella lutrensis Sacramento splittail Pogonichthys macrolepidotus carp Cyprinus carpio pikeminnow Ptychocheilus grandis golden shiner Notemigonus chrysoleucas Sacramento sucker Catostomus occidentalis rosyface shiner Notropis rubellus delta smelt Hypomesus transpacificus fathead minnow Pimephales promelas longfin smelt Spirinchus thaleichthys white catfish Ameiurus catus steelhead/rainbow trout Oncorhynchus mykiss black bullhead Ameiurus melas Chinook salmon Oncorhynchus tshawytscha channel catfish Ictalurus punctatus threespine stickleback Gasterosteus aculeatus wakasagi Hypomesus nipponensis prickly sculpin Cottus asper western mosquitofish Gambusia affinis tule perch Hysterocarpus traski inland silverside Menidia beryllina white sturgeon Acipenser transmontanus striped bass Morone saxatilis green sturgeon Acipenser medirostris bluegill Lepomis macrochirus river lamprey Lampetra ayresi redear sunfish Lepomis microlophus smallmouth bass Micropterus dolomieu
largemouth bass Micropterus salmoides
white crappie Pomoxis annularis
black crappie Pomoxis nigromaculatus
bigscale logperch Percina macrolepida
yellowfin goby Acanthogobius flavimanus
Shimofuri goby Tridentiger bifasciatus
chameleon goby Tridentiger trigonocephalus
Source: Moyle, 2002; data compiled by AECOM in 2010, in DEIS/DEIR Phase 3 of the RD 17 100-year Levee Seepage Area Project, Bio Resources, page 3.6-16.

Important attributes of the aquatic habitat within the SJR are aquatic vegetation and SRA habitat. Aquatic vegetation is represented by floating, submerged and emergent vegetation. Aquatic vegetation serves as hiding cover and an invertebrate food production base for nearly all aquatic species. The percent of aquatic vegetation cover varies throughout the study area.

The USFWS defines SRA cover as “the zone of interface of water with the land margin, projected over the water to the maximum extent of overhead vegetation” (USFWS, 2014). The habitat value within the SRA cover zone varies with factors such as water depth, overhead cover from nearby riparian trees, instream cover elements such as wood, boulders and submerged vegetation and the type of aquatic substrate. SRA cover is considered essential habitat to a variety of fish species and is used as cover, forage, spawning and rearing habitat for fishes, both anadromous species and resident native and nonnative fishes (USFWS, 2014). In this nearshore aquatic zone, overhanging trees and shrubs provide shade which is important to the survival of many aquatic organisms, including fish. Overhanging vegetation moderates water temperatures, which is an important factor for various life stages of native fish species. The vegetation provides food and habitat for both terrestrial and aquatic invertebrates, which in turn serve as food for several fish species.

Aquatic vegetation or in water cover, provides a diversity of microhabitats which allows for high species diversity, abundance and a food source for instream invertebrates, which in turn are eaten by several native fish species. Thus, a broad food base and extensive cover and habitat niches are supported by in-water cover. These values in turn create high fish diversity and abundance (USFWS, 1992).

ATTACHMENT D 1259
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San Joaquin County, CA Affected Environment and Environmental Consequences The existing overhead shade cover within the study area varies by location and along each waterway. The amount of potential SRA overhead cover within the study area was calculated using aerial photography and determining which areas have overhanging vegetation and trees adjacent to the natural channel and which areas do not. Generally, greater shade cover occurs during summer when full tree canopies are present.

Initial analysis of total lf (lf) of potential SRA was conducted using Google Earth ProTM for the various reaches associated with ETL compliance in the study area.

Subsequent to release of the Draft FR/EIS/EIR, additional investigation and coordination with the NMFS’s lead senior fisheries biologist responsible for the project area, resulted in the conclusion that the full suite of characteristics that comprise SRA are not present in Mosher, Fivemile, Fourteenmile and Tenmile sloughs and no SRA is actually present in these areas..

Central Stockton
SJR
The lower SJR serves as a migration corridor and/or provides other types of habitat (e.g., rearing, spawning) for two runs of Chinook salmon (i.e., fall-run and late fall run (Oncorhynchus tshawytscha), steelhead (Oncorhynchus mykiss), Delta smelt (Hypomesus transpacificus), Sacramento splittail (Pogonichthys macrolepidotus), white sturgeon (Acipenser transmontanus), green sturgeon (Acipenser medirostris) and numerous other resident native and nonnative species (Table 5-34) (AECOM, 2011).

In the project vicinity, the SJR is characterized as a wide channel (about 300 feet) with little riparian canopy or overhead vegetation and minimal bank cover. Aquatic habitat in the SJR is characterized primarily by slow moving glides and pools, is depositional in nature and has limited water clarity and habitat diversity.

Altered flow regimes, FRM and bank protection efforts along much of the SJR reduced riparian vegetation and associated SRA habitat, sediment transport, channel migration, avulsion and large woody debris recruitment and isolated the channel from its floodplain. This resulted in a decline in habitat quality for fish species utilizing the SJR near the project. However, fish use this segment of the river even if only as a migratory pathway to and from upstream spawning and rearing areas (AECOM, 2011).

Calaveras River
The Calaveras River, a tributary to the SJR, is a relatively small, low elevation Central Valley drainage that receives runoff mainly from winter rainfall (CDFG, 1993). Flow in the Calaveras River is regulated by New Hogan Dam, located 38 miles upstream from the river’s mouth at Stockton. New Hogan Reservoir has a storage capacity of 317,000 AF at gross pool and is operated by USACE for flood control, water supply and recreation. Rights to releases below New Hogan Dam are contracted for by the Stockton East Water District (SEWD) and the Calaveras County Water District through the Bureau of Reclamation (Stillwater Sciences, 2004).

The flow regime of the Calaveras River has been fundamentally altered since the 1930’s when regulation of the Calaveras River began, first through Hogan Dam and subsequently through New Hogan Dam.

Historically, the river’s hydrology was characterized by highly variable flows during winter months and rapid attenuation of flows in the summer. Under current flow management, the variability and magnitude of winter flows is strongly reduced, while the magnitude and consistency of summer flows has increased dramatically. Water supplies stored in New Hogan Reservoir are transferred, via the Calaveras River, to downstream locations as far as the town of Bellota, where SEWD operates a municipal water supply diversion. The effect has been to transform the lower river from a more Mediterranean system, with high intra-year variability, to one that behaves like a typical snowmelt system, with fall and winter precipitation stored and released gradually in the summer months (Stillwater Sciences, 2004).

ATTACHMENT D 1260
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San Joaquin County, CA Affected Environment and Environmental Consequences While little is known of the historical anadromous runs in the Calaveras River, currently fall Chinook salmon and steelhead (Oncorhynchus mykiss) enter the Calaveras River when suitable fall streamflows occur. The Calaveras River also supports a popular resident rainbow trout fishery. In 1998, the Central Valley steelhead Evolutionarily Significant Unit (ESU) was listed as “threatened” under the Federal (ESA by NOAA Fisheries (NMFS 1998). In June 2000, critical habitat was designated for Central Valley steelhead that included Calaveras River; however, this designation was later rescinded and critical habitat designation for Central Valley steelhead was subsequently redesignated on September 2, 2005, effective January 2, 2006 (70 FR 52488).

Stockton Diverting Canal
Currently, adult Chinook salmon and steelhead have two potential migration routes to access the Calaveras River upstream of Bellota Weir: 1) the Old Calaveras River channel downstream of Bellota and 2) Mormon Slough via the Stockton Diverting Canal. The majority of Chinook salmon and steelhead migrate through the Stockton Diverting Canal and Mormon Slough to access the mainstem Calaveras River, because this route typically receives higher flows than the Old Calaveras River channel. However, in many years, the timing and magnitude of stream flows below Bellota Weir are not sufficient to allow adult Chinook salmon and steelhead to migrate upstream into the high quality spawning and rearing habitat between Bellota and New Hogan Dam (USFWS, 1993). Additionally, numerous in-channel structures, natural hydraulic barriers and dry reaches along these migration routes create partial or complete migration barriers. For example, several hundred fall Chinook salmon were observed during the fall of 1995 at Bellota Dam, where they were temporarily blocked (CDFG, 1996).

Flow management and channelization activities have dramatically altered the sloughs and wetlands below Bellota Weir. These activities have probably reduced suitability of the lowest river reaches for salmonid rearing. For example, conditions that would not be expected to support significant numbers of rearing juveniles include: dewatering Old Calaveras River channel, complete lack of SRA habitat on the Stockton Diverting Canal and simplification and reduction of riparian cover on Mormon Slough.

RD 17
The SJR and the south bank of French Camp Slough comprise the RD 17 reach of the project area. Existing conditions for the RD 17 reach are the same as explained above for the Central Stockton reach.

ASSESSMENT METHODS AND BASIS OF SIGNIFICANCE
Assessment Methods
Existing resource information related to the project area was reviewed to evaluate whether sensitive habitats and native fish species are known from or could occur in the study area. The information reviewed included the following sources: published and unpublished documents and reports pertaining to the study area; PICES Database by University of California; CNDDB; Endangered Species Database maintained by USFWS; and Superfund reference website, Environmental Protection Agency. Analysis of total SRA overhead cover in lf (lf) was conducted using Google Earth ProTM.

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San Joaquin County, CA Affected Environment and Environmental Consequences Basis of Significance
In general, effects on fish populations are significant when the project causes or contributes to substantial short or long-term reductions in abundance and distribution. An effect is found to be significant if it:
 Interferes substantially with the movement of any native resident or migratory fish or wildlife species or with established native resident or migratory wildlife corridors or impede the use of native wildlife nursery sites;
 Has a substantial adverse effect, either directly or indirectly through habitat modifications, on any species identified as a candidate, sensitive or special status species in local or regional plans, policies or regulations or by CDFW or USFWS;
 Substantially reduces the habitat of a fish population;  Causes a fish population to drop below self‐sustaining levels;  Threatens to eliminate an animal community.

ALTERNATIVE 1 - NO ACTION
Under the No Action Alternative, no Federal action would be taken to reduce flooding. Risk to existing floodplain development would increase due to pressures presented by climate change, and seismic events.

If flood events were to occur, there is a risk of possible levee failure due to seepage, slope instability, erosion and overtopping. The chance of overtopping increases with the challenges faced by sea level rise.

Activities involved with flood fighting, levee protection and repair could cause harm to the fish populations found in the SJR system. Heavy equipment would be needed to move emergency supplies and personnel to locations along the levee system requiring emergency stabilization and repair. This heavy equipment has the potential to destroy riparian habitat used by organisms for cover and potential food sources. The chemicals, oil and fuel commonly used in this equipment could leak into the environment and the riverine system, causing injury or death to fish.

Given the unpredictable nature of emergency activities, it is unlikely BMPs and other measures could be implemented to reduce negative effects to fish populations.

In the event of the levee being compromised by overtopping, seepage or loss of bank stability, there are additional risks associated with fish populations. Straying could occur, causing a portion of distinct genetic population segments of fish to be unable to reach historical spawning grounds. When flood waters recede, fish stranding is likely to take place by adults as well as juvenile fish, reducing these populations. Levee failure would allow for the introduction of pollutants into the system. Flooding in developed urban areas would introduce a number of household chemicals, oils, fuels, pharmaceuticals organic and inorganic pollutants. These substances have multiple ways of affecting fish populations, increasing risk for mortality.

Agricultural land also presents the possibility for chemical and organic materials to enter the riverine system in the event of a levee breach. The use of herbicides, pesticides and fertilizers on soils is well known. All these chemicals have numerous ways in which they will interact in an aquatic environment, having negative impact to fish populations.

The magnitude of the impacts would depend upon the location of the levee breach, severity of the storm and river flows at the time of flooding. Predicting these events and providing a determination of significance ATTACHMENT D 1262
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San Joaquin County, CA Affected Environment and Environmental Consequences is not possible based on the information available at this time. Therefore, identification of potential effects is too speculative for meaningful consideration.

ALTERNATIVE 7A
North Stockton
As described in Chapter 4, Alternative 7a would include the construction of levee remediation measures to address: (1) Under and through seepage, (2) restoration to USACE levee design criteria, (3) erosion, (4) geometry, (5) ETL VFZ requirements, (6) seismic stability and (7) FRM identified for Mosher Slough, Shima Tract, Fivemile Slough, Fourteenmile Slough and Tenmile Slough.

Construction activities, which include erosion protection, would be placed on the landside (in what is currently agricultural land) of Shima Tract, Fivemile Slough, Fourteenmile Slough and Tenmile Slough; this work would have no effect on existing waterside habitat conditions. Therefore, erosion protection construction would not affect resident native fish population abundance, movement and distribution.

Increases in turbidity and suspended sediment associated with ground-disturbing activities are likely to extend beyond the immediate construction area and could result in short- to long-term effects of fish and aquatic resources depending on the effectiveness of the proposed erosion control measures. Under Alternative 7a, the proposed activities that are most likely to increase turbidity and sedimentation are those that disturb shoreline sediments or soils on the adjacent bank or levee where they can be carried by surface runoff to the river (e.g., clearing and grubbing of vegetation). Elevated concentrations of fine sediment and turbidity in the aquatic environment can have both direct and indirect effects on fish. The severity of these effects depends on the concentration and duration of exposure and the sensitivity of the species and life stage. Juvenile Chinook salmon, steelhead and green sturgeon are expected to be the most sensitive species and life stage in the project area.

For most activities, noise-related direct effects on fish would be limited to avoidance behavior in response to movements, noises and shadows caused by construction personnel and equipment operating in or adjacent to the water body. Resident fish would likely move upstream, downstream or laterally to an unaffected portion of the river in response to noise or disturbance and would therefore be unaffected.

The North Stockton reach would be required to establish compliance with the USACE Vegetation ETL, as explained in detail in Section 4.6; however, subsequent to release of the Draft FR/EIS/EIR, additional investigation and coordination with the NMFS’s lead senior fisheries biologist responsible for the project area, resulted in the conclusion that the full suite of characteristics that comprise SRA are not present in Mosher, Fivemile, Fourteenmile and Tenmile sloughs and no SRA is actually present in these areas.

A permanent Consu on Fourteenmile Slough could have indirect effects on native fish populations due to an increase of predatory species attracted to structure and shade for hiding, increasing the predation on native fish species. During non-operational conditions, overwater and in water structures can alter underwater light conditions and provide potentially favorable holding conditions for adult fish, including species that prey on juvenile fishes. Permanent shading from the installation of piles and other structures in Fourteenmile Slough could increase the number of predatory fish (e.g., striped bass, largemouth bass) holding in the study area and their ability to prey on resident native fish species.

Construction design and sequencing of the closure structure would have in water habitat disturbance and affect SRA, resulting in short and long term impacts on fish, including the potential for entrainment during gate closure. Final design and operational strategies would be coordinated with the resource agencies to minimize or avoid long term effects on fish species in the project area.

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San Joaquin County, CA Affected Environment and Environmental Consequences Therefore, direct and indirect effects would be significant and unavoidable due to the permanent closure structure on Fourteenmile Slough, which could have indirect effects on native fish populations due to an increase of predatory species attracted to structure and shade for hiding, increasing the predation on native fish species and the potential for entrainment during gate closure.

Central Stockton
Construction effects would be the same as those described for the North Stockton reach except for the operation of the closure structure on Smith Canal and impacts due to SRA removal.

Construction and operational effects of the Smith Canal closure structure would be the same as those described above for the Fourteenmile Slough closure structure except for the duration and timing of gate closure. The purpose of the closure structure would be to cut off high water levels during high flow events.

Operation of the closure structure would limit the water saturation levels in Smith Canal, which would reduce the risk of levee damage during flood events. The closure structure gates would be closed during high water levels on the SJR, typically during a flood event. Due to the tidal influence of the Delta region, there is the potential that these high water events could last from a few days to a few months, depending on river conditions. Construction design and sequencing of the closure structure would have in water habitat disturbance, affect SRA and result in short- and long-term impacts on fish including potential entrainment during gate closure. Final design and operational strategies would be coordinated with the resource agencies to minimize or avoid long-term effects on fish species in the project area.

The Central Stockton reach would also be required to establish compliance with USACE ETL vegetation requirements, as explained in detail in Section 4.7. A total of 19,630 lf of SRA habitat located on the Calaveras River, SJR, French Camp Slough and Duck Creek would be removed. Therefore, there would be significant direct effects by reducing the available areas for shade and possible food sources available to the existing native and nonnative fish species present in the study area. Direct and indirect effects due to loss of SRA habitat including potential entrainment during gate closure would be significant and unavoidable even with mitigation that included a variance to the Vegetation ETL and on-site compensation plantings. This is because of the temporal impacts that would occur between the time vegetation was removed and the time that new vegetation matured to a point that it provided off-setting ecosystem services.

There would be permanent impacts where constructed FRM features preclude revegetation after construction is complete.

ALTERNATIVE 7B
Alternative 7b direct and indirect effects due to construction for the North Stockton and Central Stockton reaches would be the same as Alternative 7a, but would include levee remediation measures for RD 17.

RD 17
Construction effects for the RD 17 reach would be the same as those described above for Alternative 7a for the North Stockton Reach.

The RD 17 reach would be required to establish compliance with USACE vegetation requirements, as explained in detail in Section 4.6. Removal of 31,698 lf of SRA habitat located on the SJR and French Camp Slough would result in significant direct effects by reducing the available areas for shade and possible food sources available to the existing native and nonnative fish species present in the study area. Indirect effects to loss of SRA habitat would be significant and unavoidable.

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San Joaquin County, CA Affected Environment and Environmental Consequences ALTERNATIVE 8A
The Alternative 8a direct and indirect effects due to construction for the North Stockton and Central Stockton reaches would be the same as those described above for Alternative 7a except for an extension of levee remediation on the Calaveras River and levee remediation on the Stockton Diverting Canal.

The new levee construction on Duck Creek would involve 1,283 lf, of which 613 lf would be located next to the water of Duck Creek. There is no SRA habitat located here and water conditions would suggest nonnative fish species tolerant of high water temperatures and low dissolved oxygen would be the only species present.

This alternative would result in indirect effects due to loss of SRA habitat that would be significant and unavoidable even with mitigation that included a variance to the Vegetation ETL and on-site compensation plantings, because of the temporal impacts that would occur between the time vegetation was removed and the time that new vegetation matured to a point that it provided off-setting ecosystem services. There would be permanent impacts where constructed FRM features preclude revegetation after construction is complete.

ALTERNATIVE 8B
Alternative 8b direct and indirect effects due to construction for the North Stockton, Central Stockton and RD 17 reaches would be the same as Alternative 7b except for an extension of levee remediation on the Calaveras River and levee remediation on the Stockton Diverting Canal. Direct and indirect effects due to loss of SRA habitat would be significant and unavoidable even with mitigation that included a variance to the Vegetation ETL and on site compensation plantings, because of the temporal impacts that would occur between the time vegetation was removed and the time that new vegetation matured to a point that it provided off-setting ecosystem services. There would be permanent impacts where constructed FRM features preclude revegetation after construction is complete.

ALTERNATIVE 9A
The effects of Alternative 9a from construction and operation for the North Stockton and Central Stockton reaches would be the same as described for Alternative 7a. However, Alternative 9a includes the additional effects from the proposed Mormon Channel Control Structure and Bypass Channel.

The Mormon Channel measure consists of construction and operation of a control structure and channel improvements to allow for up to 1,200 cfs of flood flows to be diverted down this channel. The control structure includes a tainter gate that would be operated to divert water into the Mormon Channel during high water events. The gates would likely be operated every 2 years or so. The amount of water and duration of diverted flows would be adjusted according to the total flows moving through the system.

A FRM bypass system like this would likely only provide a corridor for migrating adult and juvenile fish, with no habitat for spawning or protection from predators. The 1,200 cfs could potentially be enough for attraction flows for fish migration up the Mormon Channel. Fish passage facilities located at the Stockton Diverting Canal could be considered in future planning. Due to the possibility of native and nonnative fish species in the Mormon Channel after a storm event, ramping down flows in the Mormon Channel so fish can escape to the main stem SJR before getting isolated in pockets and pools once flows are no longer being released would be implemented. Construction design and sequencing of the closure structure would have in water habitat disturbance and affect SRA, resulting in short and long term impacts on fish. Final design and operational strategies would be coordinated with the resource agencies to minimize or avoid long term effects on fish species in the project area.

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San Joaquin County, CA Affected Environment and Environmental Consequences Direct and indirect effects due to loss of SRA habitat would be significant and unavoidable even with mitigation that included a variance to the Vegetation ETL and on site compensation plantings. This is because of the temporal impacts that would occur between the time vegetation was removed and the time that new vegetation matured to a point that it provided off-setting ecosystem services. There would be permanent impacts where constructed FRM features preclude revegetation after construction is complete.

ALTERNATIVE 9B
The effects of Alternative 9b from construction and operation for the North Stockton, Central Stockton and RD 17 reaches would be the same as those described for Alternative 7b. Direct and indirect effects due to loss of SRA habitat would be significant and unavoidable even with mitigation that included a variance to the Vegetation ETL and on site compensation plantings, because of the temporal impacts that would occur between the time vegetation was removed and the time that new vegetation matured to a point that it provided off-setting ecosystem services. There would be permanent impacts where constructed FRM features preclude revegetation after construction is complete.

MITIGATION
Mitigation measures, including avoidance and minimization associated with SRA and riparian habitat, are addressed in VEGETATION (Section 5.9,) and WILDLIFE (Section 5.10), while measures with related BMPs associated with construction-related impacts such as dust, stormwater runoff and spills are addressed in WATER QUALITY (Section 5.5). Additional mitigation associated with impacts to fisheries is identified:
 In-water construction not associated with the closure structures would be restricted to the August 1 through November 30 work window, during periods of low fish abundance and outside the principal spawning and migration season. The typical construction season would generally correspond to the dry season, but construction may occur outside the limits of the dry season, only as allowed by applicable permit conditions.
 Due to the deleterious effects of numerous chemicals on native resident fish used in construction, if a hazardous materials spill does occur, a detailed analysis will be performed immediately by a registered environmental assessor or professional engineer to identify the likely cause and extent of contamination. This analysis will conform to American Society for Testing and Materials standards and will include recommendations for reducing or eliminating the source or mechanisms of contamination. Based on this analysis, USACE and its contractors would select and implement measures to control contamination, with a performance standard that surface water quality and groundwater quality must be returned to baseline conditions.  During design feasibility studies for the operation and maintenance of the Mormon Channel bypass, the parameters would be to avoid or minimize stranding in the channel after flow events and flushing of upstream migrating adult fish down the channel from the Stockton Diverting Canal.

Designs would include but not be limited to either an adult fish passage barrier at the confluence of the Stockton DWSC or for fish passage facilities at the Stockton Diverting Canal.

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San Joaquin County, CA Affected Environment and Environmental Consequences  All in water construction activities would be limited to the period of June 1 through October 31 to avoid the primary migration periods of listed salmonids.  In-water pile driving would be restricted to the period of July 1 through September 30 to avoid or minimize exposure of adults and juvenile salmonids to underwater pile-driving sounds.  All pile driving would be conducted by a vibratory pile driver to minimize underwater sound levels during pile driving operations.
 Pile driving would be conducted by barge to minimize disturbance of riparian habitat.

While mitigation, including BMPs, would reduce effects on fisheries, impacts would nevertheless remain significant and unavoidable due to affects associated with vegetation removal and construction of the closure structures.

SPECIAL STATUS SPECIES
This section describes special status species that either occur or have the potential to occur in the project area that may be potentially impacted by the project.

ENVIRONMENTAL SETTING
Regulatory Framework
Federal
 Bald and Golden Eagle Protection Act (16 U.S.C. 668-668c)  CWA
 Federal ESA (16 U.S.C. 1531 et seq.)
 Magnuson-Stevens Fishery Conservation and Management Act  Migratory Bird Treaty Act (16 U.S.C. §703-712)
State
 California ESA (Fish and Game Code 2050 et seq.)
 CFGC Section 1600: Streambed Alteration Agreements
 California Native Plant Protection Act (Fish and Game Code 1900 et seq.) Existing Conditions
Information on special status species that may be affected was gathered from various sources:
 USFWS online services species list (USFWS, accessed on 23 April 2014);  CDFW’s CNDDB (CDFG, 2014);
 California Native Plant Society’s (California Native Plant Society, 2014) online Inventory of Rare and Endangered Vascular Plants of California (California Native Plant Society).

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San Joaquin County, CA Affected Environment and Environmental Consequences Each database query for special-status species was based on a search of the USGS 7.5’ quadrangles on which the study area is located (i.e., Waterloo [478C]), Lodi South [479D], Stockton East [461B], Stockton West [462A], Lathrop [462D], Manteca [461C]. The resulting USFWS queries, as well as the lists generated by the CNDDB and CNPS searches, are included in the Environmental Addendum. All lists were reviewed and habitat preferences for each species were compared with the affected areas and project site description.

Those special status species known to occur or with suitable habitat, in or near the project area, are identified in Table 5-35 and discussed in detail below.

Certain special status species and their habitats are protected by Federal, State or local laws and agency regulations. The Federal ESA of 1973 (50 CFR 17) provides legal protection for plant and animal species in danger of extinction and is administered by USFWS and NMFS. The California ESA of 1977 parallels the Federal ESA and is administered by CDFW. Other special status species lack legal protection, but have been characterized as “sensitive” based on policies and expertise of agencies or private organizations or policies adopted by local government. Special-status species are those that meet any of the following criteria:
 Listed or candidate for listing under the Federal ESA (50 CFR 17);  Listed or candidate for listing under California ESA;  Nesting bird species and active nests of birds listed under the Migratory Bird Treaty Act;  Species listed in the Bald and Golden Eagle Protection Act;  Essential Fish Habitat (EFH) listed under the Magnuson-Stevens Act;  Fully protected or protected species under stated CDFW code;  Wildlife species of special concern listed by the CDFW;  Plant species listed as Rare under the California Native Plant Protection Act;  Plant species listed by the California Native Plant Society; and  Species protected by other local ordinances, goals and policies.

Lists of special status species and candidate species were found on the USFWS website and the CNDDB.

The USFWS and CNDDB lists are included in the Environmental Addendum and are summarized in Table 5-35.

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San Joaquin County, CA Affected Environment and Environmental Consequences Table 5-35: Special Status Species and Critical Habitats Species/Critical
Habitat Status1 Potential to Occur2

INVERTEBRATES
Valley elderberry
longhorn beetle
Desmocerus
californicus
dimorphus
Federal:

T
May occur; elderberry shrubs present occasionally along SJR on the waterside and landside of the project area
Vernal pool fairy
shrimp
Branchinecta
lynchi
Federal:

T
Unlikely to occur
No known habitat in the project area.

No NDDB records in the project area.

Vernal pool
tadpool shrimp
Lepidurus
pachardi
Federal:

T
Unlikely to occur
No known habitat in the project area.

No NDDB records in project area.

AMPHIBIANS
California Tiger
Salamander
Ambystoma
californiense
Federal:

T
CA: T
Unlikely to occur; potential aquatic habitat is limited to one constructed pond in RD 17, likely with predatory fish; a small area of fresh water marsh and agricultural ditches. A 1996 CNDDB record documents California tiger salamander adjacent to Hwy 120 in roadside seasonal wetland, however, it is two miles east of the SJR and geographically isolated.

California redlegged frog
Rana draytonii
Federal:

T
CA: T
Unlikely to occur
No CNDDB records in project area.

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San Joaquin County, CA Affected Environment and Environmental Consequences

REPTILES
Giant garter
snake
Thamnophis
gigas
Federal:

T
CA:

SSC
May occur; suitable habitat is present in backwater areas of the adjacent SJR and in agricultural ditches with permanent water. The CNDDB listed one occurrence of GGS within the Central Stockton project area in the Stockton Diverting Canal.

Western pond
turtle
Actinemys
marmorata
CA:

SSC
May occur; suitable habitat is present in backwater areas of the adjacent SJR and in agricultural ditches with permanent water.

MAMMALS
Riparian brush
rabbit
Sylvilagus
bachmani
riparius
Federal:

E
State: E
Known to occur; occupied riparian habitat is present on the waterside of and suitable habitat is present immediately adjacent to the project area in several elements; species is also known to occur at an oxbow of RD 17.

Western mastiff
bat
Eumops perotis
californicus
State:

SSC May occur; suitable foraging habitat present, but no potential roost sites.

Red bat
Lasiurus
blossevillii
State:

SSC May occur; suitable foraging and roosting habitat present.

BIRDS
Tricolored
Blackbird
Agelaius tricolor
State:

SSC
May occur; foraging habitat present in small areas of freshwater marsh and riparian habitat. Five occurrences have been documented within the RD 17 project area. Five occurrences exist within the project footprint at RD 17. One occurrence exists south of Howard road one-half mile east of the project area. Two occurrences exist one-half mile west of Interstate 5 and the SJR. Two additional occurrences exist at the southern end of the project area more than one mile away.

Burrowing owl
Athene
cunicularia
State:

SSC
May occur; suitable foraging and nesting habitat present; One burrowing owl occurrence is present at Mosher Slough. Two burrowing owl occurrences are present at a railyard facility three-quarter mile east of the project area. Five burrowing owl occurrences are present at in the northern project area of RD 17 in a residential development of the Taft ATTACHMENT D 1270
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San Joaquin County, CA Affected Environment and Environmental Consequences Mosswood area. The occurrences are one-half mile from the project area at the SJR, Old Mormon Slough and Developable Lands (RD 17).

Swainson’s
hawk
Buteo swainsoni
State: T
Known to occur; suitable foraging habitat and nesting habitat present in and adjacent to the project area. Six occurrences have been documented within the Delta Front/North Stockton project area. Two occurrences exist within the project footprint at Mosher Slough and Calaveras-Right.

One occurrence exists at Calaveras-Right within 0 to 100 feet of the project area. Two occurrences exist within 101-500 feet from the project at Mosher Slough at Shima Tract and Calaveras-Right. Three occurrences exist within 501 feet to .5 miles at Shima Tract, Fourteenmile Slough Dry Land Levee and Calaveras-Right. Eight occurrences have been documented within the Central Stockton project area. Three occurrences exist within the project footprint at SJR Mile, French Camp Slough and Duck Creek. One occurrence exists within 101-500 feet from the project area at Calaveras-Left. Four occurrences exist within 501 feet to .5 miles at Calaveras Left, SJR and Smith Canal. Eight occurrences have been documented within the RD 17 Area. Four occurrences exist within the project footprint at French Camp Slough-Left, SJR Mile X and Y and the Developable Lands. Three occurrences exist within 0 feet to 100 feet at SJR RD 17 and Old Mormon Slough. Three occurrences exist within 101- 500 feet at SJR RD 17 and Old Mormon Slough. Six occurrences exist within 501 feet to 0.5 miles at French Camp Slough-Left, SJR Mile (4) and Old Mormon Slough.

White-tailed kite
Elanus leucurus
State: FP May occur; suitable foraging and nesting habitat present in and adjacent to the project area
Song sparrow
("Modesto"
population)
Melospiza
melodia
State:

SSC
May occur; suitable foraging and nesting habitat present in and adjacent to the project area
Least Bell's
vireo
Vireo bellii
pusillus
Federal:

E
State: E
May occur; suitable foraging and nesting habitat present in and adjacent to the project area - Riparian forest, Riparian scrub, Riparian woodland.

Yellow-headed
blackbird
Xanthocephalus
State:

SSC
May occur; Three occurrences have been documented within the RD 17 southern project area. One occurrence exists within 501 feet to .5 miles.

Two occurrence exist within >.5 miles and <1 mile.

PLANTS
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San Joaquin County, CA Affected Environment and Environmental Consequences Alkali milkvetch
Astragalus tener
CNPS:
1B.2
May occur; 2 accounts – one on project site, the other within 100-500 feet of the project site within Central Stockton. Recorded as extirpated.

Heartscale
Atriplex
cordulata var.
cordulata
CNPS:
1B.2
Unlikely to occur; found in saline or alkaline soils in chenopod scrub, meadows and seeps, sandy areas in valley and foothill grassland.

San Joaquin
spearscale
Atriplex
joaquinana
CNPS:
1B.2
Unlikely to occur; found in alkaline soils in chenopod scrub, meadows and seeps, playas, valley and foothill grassland.

Round-leavd
filaree
California
Macrophylla
CNPS:
1B.1
Unlikely to occur; Clay soils in cismontane woodland, valley and foothill grassland.

Owl’s clover
Castilleja
campestris ssp.
succulent
Federal:

T
State: E
Unlikely to occur; (hemiparasitic) on the roots of other plants. It occurs on the margins of vernal pools, swales and some seasonal wetlands, often on acidic soils. It is never dominant and it is found in only a few of the pools in an area. Known to occur in adjacent quad north of project.

Slough thistle
Cirsium
crassicaule
CNPS: 2 May occur; 3 on site accounts in RD 17. Chenopod scrub, marshes and swamps (sloughs), riparian scrub.

Big tarplant
Blepharizonia
plumose
CNPS:
1B.1
May occur; Big tarplant occurs in annual grassland on clay to clay-loam soils, usually on slopes and often in burned areas, below 1,500 feet 2 accounts – one on project site, the other within 100-500 feet of the project site at Old Mormon Slough. Recorded as extirpated.

Watershield
Brasenia
schreberi
CNPS:
2B.3
Unlikely to occur; Water Shield is an aquatic plant with slender, branching stems. The Leaves are entire, floating, oval to elliptic in shape, green above, often purple beneath, long-stemmed and have the stalk or petiole attached.

Palmate-bracted
bird’s-beak
Chloropyron
palmatum
Federal:

E
State: E Unlikely to occur; Alkaline grassland, alkali meadow, chenopod scrub; ATTACHMENT D 1272
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San Joaquin County, CA Affected Environment and Environmental Consequences Delta button
celery
Eryngium
racemosum
CNPS:
1B
State: E
Unlikely to occur; in low-quality irrigation ditch and freshwater marsh habitat; 1892 and 1913 herbarium records are only source of occurrences (near SJR and I-5 crossing); thought to be possibly extirpated Rose mallow
Hibiscus
lasiocarpus
CNPS: 2
May occur; 2 accounts in Delta Front/North Stockton, one in Central Stockton. Native to riparian areas around the Sacramento River in California and can also be found in other states. Grows in moist soil near the river
Delta tule pea
Lathyrus
jepsonii var.
jepsonii
CNPS:
1B
May occur; 3 accounts in Central Stockton within 100 to 500 feet of project area. Freshwater and brackish marshes and swamps.

Mason’s
lilaeopsis
Lilaeopsis
masonii
CNPS:
1B
State: R
May occur; 3 accounts in Delta Front/North Stockton Riparian scrub, brackish or freshwater marshes and swamps.

Delta mudwort
Limosella
subulata
CNPS: 2 Unlikely to occur; Marshes and swamps.

Sanford’s
arrowhead
Sagittaria
sanfordii
CNPS:
1B
Unlikely to occur; Freshwater marshes, sloughs, canals and other slowmoving water habitats.

Suisun marsh
aster
Symphyotrichum
lentum
CNPS:
1B
Unlikely to occur; 1892 (near City of Lathrop) and 1920 (near town of Banta) herbarium records are only source of occurrences. Brackish and freshwater marshes and swamps.

Wright’s
trichocoronis
Trichocoronis
wrightii var.
wrightii
CNPS: 2
Unlikely to occur; Herbarium records from 1892 to 1914 are only source of occurrences (near SJR and I-5 crossing) On alkaline soils in floodplains, meadows and seeps, marshes and swamps, riparian forest, vernal pools.

FISH
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San Joaquin County, CA Affected Environment and Environmental Consequences Central Valley
steelhead
Oncorhyncus
mykiss
Federal:

T
State: **
May occur; Occurs in the Sacramento and SJRs, tributaries and Delta.

Occurs seasonally in the SJR in the project vicinity.

Central Valley
fall-/late fall -run
Chinook salmon
Oncorhyncus
tshawytscha
Federal:

SC
State:

SSC
May occur; Occurs in the Sacramento and SJRs, tributaries and Delta.

Has potential to occur in the SJR in the project vicinity.

Sacramento
River winter-run
Chinook salmon
Oncorhyncus
tshawytscha
Federal:

E
State: E
Unlikely to occur; Occurs in the Sacramento River, tributaries and Delta.

Considered but not included due to only potential presence lower down at the confluence of the San Joaquin and Sacramento Rivers. No presence expected in the action area.

Central Valley
spring-run
Chinook salmon
Oncorhyncus
tshawytscha
Federal:

T
State: T
Unlikely to occur; Occurs in the Sacramento River, tributaries and Delta.

Considered but not included due to extirpation on the SJR.

Green sturgeon
Acipenser
medirostris
Federal:

T
State: **
May occur; Occurs in the Sacramento River and San Joaquin, Sacramento River Delta. Has the potential to occur in the SJR in the project vicinity.

Delta smelt
Hypomesus
transpacificus
Federal:

T
State: T
May occur; Occurs in tidally influenced segments of the Sacramento and SJRs, tributaries and Delta. Has potential to occur in the SJR in the project vicinity.

Longfin smelt
Spirinchus
thaleichthys
Federal:
**
State: T
Unlikely to occur; Occurs in tidally influenced segments of the Sacramento and SJRs, tributaries and Delta. Has potential to occur in the SJR in the project vicinity.

Sacramento
splittail
Pogonichthys
macrolepidotus
Federal:

DT
State:

SSC
Unlikely to occur; Occurs in the Sacramento and SJRs, tributaries and Delta. Has potential to occur in the SJR in the project vicinity.

Hardhead
Mylopharodon
conocephalus
Federal:
**
State:

SSC
Unlikely to occur; Occurs in the Sacramento and SJRs, tributaries and Delta. Has potential to occur in the SJR in the project vicinity.

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San Joaquin County, CA Affected Environment and Environmental Consequences San Joaquin
roach
Lavinia
symmetricus sp.

Federal:
**
State:

SSC
Unlikely to occur; Occurs in tributaries to the Sacramento and SJRs. Not likely to occur in the SJR in the project vicinity.
1 Legal Status Definitions:

Federal Listing Categories
(USFWS & NMFS)
E - Endangered (legally
protected)
T - Threatened (legally
protected)
DT - Delisted from
threatened status
SC - Species of Concern
State Listing Categories (CDFW)
E - Endangered (legally protected)
T - Threatened (legally protected)
SSC - California Species of Special Concern (no formal protection) Source: CNDDB, 2014, USFWS and NMFS 2014 and AECOM 2011 2 This table focuses on known or potential presence within and adjacent to, the construction footprint for the structural FRM features.

Special Status Wildlife Species
Of the special status wildlife species identified in Table 5-35, only 10 potentially occur in the project area.

Valley Elderberry Longhorn Beetle
Status. The valley elderberry longhorn beetle (Desmocerus californicus dimorphus) (VELB) is Federallylisted as threatened. The species has no State status (the State of California does not list insects).

Distribution and Habitat. The VELB is endemic to the Central Valley and is found in riparian habitats and associated uplands where the elderberry (sambucus spp.), the beetle’s food plant, grows. The beetle is a pith-boring species that depends on elderberry plants during its entire life cycle. Larvae feed on tree pith, while adults eat the foliage and possibly the flowers of the plants. The adult stage of the VELB is shortlived, and most of the life cycle is spent in the larval stage. Eggs are laid singly or in small groups, in crevices in elderberry bark and hatch in about 10 days. Larvae bore into the pith of elderberry roots, branches, and trunks to create an opening in the stem within which they pupate, remaining in this stage for one to two years before emerging as adults. After metamorphosing into an adult, the VELB chews a circular exit hole through which it emerges, sometime during the period of late March to June. The adults are active from early March through early June with mating occurring in May. It has been suggested that the VELB is a poor disperser, based on the spatial distribution of occupied shrubs (USFWS, 1997).

Potential for Occurrence in Project Area. Elderberry shrubs are known to occur along the SJR, on both the waterside and landside of levees. Subsequent to releasing the Draft FR/EIS/EIR, a protocol-level field survey was completed within the Alternative 7a project area. Results are described below.

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San Joaquin County, CA Affected Environment and Environmental Consequences North Stockton
During a protocol-level field survey within the Alternative 7a project area. This survey identified 8 elderberry shrubs (0 nonriparian and 8 riparian) within the Alternative 7a North Stockton project area. Refer to Table 5-36 for quantities. The surveys were conducted in accordance with the Conservation Guidelines for the Valley Elderberry Longhorn Beetle (USFWS, 1999). All elderberry shrubs with the potential to be affected by project activities have been mapped and surveyed to determine the size of the stems on each shrub, location of shrubs to riparian habitat and presence of exit holes.

Central Stockton
During a protocol-level field survey within the Alternative 7a project area. This survey identified 36 elderberry shrubs (28 nonriparian and 8 riparian) within the Alternative 7a Central Stockton project area.

Refer to Table 5-36 for quantities. The surveys were conducted in accordance with the Conservation Guidelines for the Valley Elderberry Longhorn Beetle (USFWS, 1999). All elderberry shrubs with the potential to be affected by project activities have been mapped and surveyed to determine the size of the stems on each shrub, location of shrubs to riparian habitat and presence of exit holes.

RD 17 Area
A total of 25 elderberry shrubs were observed within 100 feet of the RD 17 Levee Stability Program, Phase 3 Project Area, including 16 shrubs on the waterside of the levee and 9 shrubs on the landside of the levee.

None of the shrubs had evidence of adult beetle exit holes (USACE, 2011).

Giant Garter Snake
Status. The GGS (Thamnophis gigas) is Federal and State-listed as threatened.

Distribution and Habitat. The GGS is endemic to wetlands in the Sacramento and San Joaquin valleys (Hansen and Brode, 1980). The current distribution extends from near Chico in Butte County south to the Mendota Wildlife Area in Fresno County. No occurrences of GGS are known from the northern portion of the San Joaquin Valley to the eastern fringe of the Sacramento-SJR Delta, where the floodplain of the SJR is limited to a relatively narrow trough (Hansen and Brode, 1980, 58 FR 54053). The resulting gap of 60 miles separates the southern and northern populations (Hansen and Brode, 1980, CNDDB, 2011).

Rice fields and their adjacent irrigation and drainage canals and ditches, serve an important role as aquatic habitat for the snakes. During the summer, some snakes use the flooded rice fields as long as their prey is present in sufficient densities. In late summer, rice fields provide important nursery areas for newborns. In late summer/fall, water is drained from the rice fields and the snakes become concentrated in the remaining pockets of standing water, which allow the snakes to gorge on remaining prey before the winter, their period of winter inactivity (USFWS, 1999). It appears that the majority of the snakes move back into the canals and ditches as the rice fields are drained, although a few may overwinter in the fallow fields where they hibernate within burrows in the small berms separating the rice checks (Hansen, 1998).

Potential for Occurrence in Project Area. Suitable habitat within the project area is present. Numerous sloughs, canals, low gradient streams and freshwater marsh habitats and irrigation ditches exist where a prey base of small fish and amphibians are present. Grassy banks and emergent vegetation for basking and areas of high ground protected from flooding during winter is present. One occurrence in project area has been recorded.

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San Joaquin County, CA Affected Environment and Environmental Consequences North Stockton
No occurrences.

Central Stockton
The CNDDB listed one occurrence of GGS within the Central Stockton project area in the Stockton Diverting Canal.

RD 17 Area
No occurrences.

Western Pond Turtle
Status. The western pond turtle (Emys marmorata) is a California Species of Special Concern.

Distribution and Habitat. The western pond turtle is found west of the Sierra-Cascade crest from western Washington to northwest Baja California (Stebbins, 2003). Western pond turtles inhabit fresh or brackish water habitats characterized by areas of deep water, low flow velocities, moderate amounts of riparian vegetation, warm water and/or ample basking sites and underwater cover elements such as large woody debris and rocks. Along major rivers, western pond turtles are often concentrated in areas of optimal habitat, often in side channel and backwater areas. Turtles may move to off-channel habitats, such as oxbows, during periods of high flows (Holland, 1994).

Although adults are habitat generalists, hatchlings and juveniles require very specialized habitat for survival through their first few years. Hatchlings spend much of their time feeding in shallow water with dense, submergent or short emergent vegetation (Jennings and Hayes, 1994). Habitats preferred by juveniles are relatively scarce and subject to disturbance (Jennings et al., 1992). Although an aquatic reptile, western pond turtles spend time on land basking, overwintering and nesting, up to 1 km (0.6 mi) away from aquatic habitats (Holland, 1994).

Western pond turtle eggs are typically laid in June and July, though may be laid as early as late April and as late as August (Holland, 1994). Nests are generally located in grassy meadows, away from trees and shrubs (Holland, 1994), with canopy cover commonly less than 10 percent. Incubating eggs are extremely sensitive to increased soil moisture that can cause high mortality. Egg-laying sites vary from sandy shoreline to forest soil. Young hatch in late fall or overwinter in the nest and emerge in early spring.

Although considered to be just 1 widely distributed species, it is likely that the pond turtle is a complex of closely related subspecies, each adapted for a different region. The western pond turtle is still common enough in the Delta watershed so that it is not difficult to find them in habitats ranging from sloughs of the Delta and Suisun Marsh, to pools in small streams. The problem is that the ones most seen are large, old individuals; hatchlings and small turtles are increasingly rare. The causes of the poor reproductive success are not well understood, but factors that need to be considered include elimination of suitable breeding sites, predation on hatchlings by nonnative predators (e.g., largemouth bass, bullfrogs), predation on eggs by nonnative wild pigs, diseases introduced by nonnative turtles and shortage of safe upland over-wintering refuges. If present trends continue, the western pond turtle will deserve listing as a threatened species (it may already) (CALFED, 2000).

Potential for Occurrence in the Project Area. The CNDDB does not list occurrences of western pond turtle in the project areas. However, suitable habitat is present in the backwater areas of the adjacent SJR and agricultural ditches with permanent water.

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San Joaquin County, CA Affected Environment and Environmental Consequences Riparian Brush Rabbit
Status. Riparian brush rabbit (Sylvilagus bachmani) is Federally-listed and State-listed as endangered.

Distribution and Habitat. Riparian brush rabbit occupies relatively large patches in riparian forests with a dense understory shrub layer. This species is closely tied to brushy cover and rarely moves more than a meter from cover. They will not cross large, open areas, which limits their dispersal capabilities (USFWS, 1998) and this inability to disperse beyond the dense brush makes them susceptible to mortality during flood events (USFWS, 1998; Williams, 1988). The primary threat to their survival is the limited extent of its existing habitat, extremely low numbers of individual animals and few extant populations.

Historically, riparian brush rabbits inhabited dense, brushy areas of Valley riparian forests, marked by extensive thickets of wild rose, blackberries and willows (Sandoval et al., 2006). Suitable habitat for riparian brush rabbits is characterized by an abundance of woody ground litter, mats of low-growing vines and shrubs and areas of higher ground not subject to regular or heavy flooding (Sandoval et al., 2006).

Riparian brush rabbits forage along the edges of shrub cover and in small clearings in the vegetation cover rather than in large openings, feeding on herbaceous vegetation such as grasses, sedges, clover, forbs and buds, bark and leaves of woody plants (Sandoval et al. 2006; USFWS, 1998). This species has a small home range and mainly remains hidden under protective shrub cover, seldom venturing more than 1 meter (3.3 ft) from cover (Sandoval et al., 2006).

Potential for Occurrence in the Project Area. Suitable riparian brush rabbit habitat exists with the project area. Pockets of riparian plant communities with shrub cover and in small clearings could provide suitable habitat. The species is currently restricted to several populations at Caswell Memorial State Park, near Manteca in San Joaquin County; along the Stanislaus River; on private lands adjacent to the SJR National Wildlife Refuge (Williams, 1993; Williams and Basey, 1986); along Paradise Cut, a channel of the SJR; on an oxbow along the SJR within RD 17 jurisdiction edges of shrub cover and in small clearings in the vegetation cover. The Riparian Brush rabbit does not occur in the North or Central Stockton reaches.

RD 17 Area
Documented occurrences of riparian brush rabbit within RD 17 exist. A managed preserve for brush rabbits was established in 2004. The SJR Oxbow Preserve is a 30 acre riparian forest preserve located adjacent to the SJR within the city of Lathrop, in San Joaquin County. The preserve was created in 2004 by Union Pacific Homes as mitigation for their development in the city of Lathrop (CNLM, 2014).

Western Red Bat
Status. The western red bat (Lasiurus blossevillii) is a California Species of Special Concern.

Distribution and Habitat. Western red bats have been observed near the Pacific Coast, Central Valley and the Sierra Nevada. Usually found at lower elevations, recent acoustic surveys in California have documented that western red bats, while relatively rare, are broadly distributed at elevations up to 8,202 feet in the Sierra Nevada (Pierson et al., 2000, 2001; Pierson and Rainey, 2003). They have often been observed in edge habitats—near streams, fields orchards or urban areas (Zeiner et al., 1990b). This species roosts non-colonially in dense canopies and within tree foliage, beneath overhanging leaves (Constantine, 1959, Shump and Shump, 1982), from 2 to 40 feet above ground level (Zeiner et al., 1990b). Studies in the Central Valley found that summering populations of red bats are substantially more abundant in remnant riparian stands of cottonwood or sycamore greater than 164 feet wide, than in younger, less extensive stands (Pierson et al. 2000).

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San Joaquin County, CA Affected Environment and Environmental Consequences Western red bats may forage up to 0.3 to 0.6 of a mile from their day roost (Zeiner, 1990b) at both canopy height and low over the ground (Shump and Shump, 1982). This species feeds primarily on small moths but its diet may include a variety of other insects such as crickets, beetles and cicadas (Zeiner et al., 1990b).

Western red bats mate in August and September. Breeding females have the same cover requirements as for other roost sites and with cottonwood/sycamore riparian habitat along large river drainages in the Central Valley (Ziener et al., 1990b, Pierson and Rainey, 2003). Fertilization is delayed until March or April. After an 80-to 90-day gestation period, pups are born from late May through early July.

Potential for Occurrence in the Project Area. Western red bats may roost near the study area in trees and may forage in the nearby fields. CNDDB states that suitable foraging and roosting habitat is present and the species potentially could occur.

Western mastiff bat
Status. The western mastiff bat (Eumops perotis californicus) is a California Species of Special Concern.

Distribution and Habitat. Occurs along the western Sierra primarily at low to mid-elevations and widely distributed throughout the southern Coast Ranges. Recent surveys have detected the species north to the Oregon border. Found in a wide variety of habitats from desert scrub to montane conifer. Roosts and breeds in deep, narrow rock crevices but also may use crevices in trees, buildings and tunnels. Uncommon in the Central Valley and roost sites primarily associated with crevices in cliff faces and boulders.

Potential for Occurrence in the Project Area. No occurrences were recorded within 5 miles of the affected area. CNDDB states that suitable foraging is present but roosting habitat is not. The species potentially could occur.

Burrowing Owl
Status. The burrowing owl (Athene cunicularia) is California state species of concern.

Distribution and Habitat. Burrowing owls historically ranged throughout the Central Valley, in suitable habitat in coastal areas from Marin County to the Mexican border, and in lower numbers in desert areas of the northeastern and southeastern portions of California. Throughout the vast majority of the burrowing owl's range, breeding owls persist in only small, declining populations that are highly susceptible to extirpation.

Western burrowing owls prefer open grasslands and shrublands with perches and burrows. They usually live and nest in the old burrows of California ground squirrels or other small mammals (Zeiner et al., 1990), but also can nest in piles of wood or other debris. Burrows can be found on the sides of hills, along roadside embankments, on levees, along irrigation canals, near fence lines and on or near other raised areas of land.

The breeding season for burrowing owls extends from February 1 through August 31 (CDFG, 2012).

Burrowing owls tend to be opportunistic feeders, with large arthropods, mainly beetles and grasshoppers, comprising a large portion of their diet. The species is primarily crepuscular (active at dusk and dawn) but will hunt throughout a 24-hour period.

Potential for Occurrence in the Project Area. Borrowing owls may have the potential to occur on the project site. According to the CNDDB, suitable foraging and nesting habitat is present in the project area.

North Stockton
One burrowing owl occurrence is present at Mosher Slough.

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Two burrowing owl occurrences are present at a railyard facility 0.75 miles east of the project area.

RD 17 Area
Five burrowing owl occurrences are present in the northern portion of RD 17 in the Weston Ranch residential development of the Taft Mosswood area. The closest occurrence to the RD 17 levee on the SJR is about 0.2 miles to the east. The closest occurrence to the French Camp Slough levee in RD 17 is about

1.5 miles to the south of the levee.

Swainson’s Hawk
Status. Swainson’s hawk (Buteo swainsoni) is State-listed as threatened.

Distribution and Habitat. In the Central Valley, Swainson’s hawks usually nest in large native trees, such as valley oak, cottonwood, walnut and willow and occasionally in nonnative trees, such as eucalyptus. Nests occur in riparian woodlands, roadside trees, trees along field borders, isolated trees, small groves and on the edges of remnant oak woodlands. Narrow bands of remnant riparian forest along drainages contain most of the known nests in the Central Valley (Estep, 1984; Schlorff and Bloom, 1984; England et al., 1997).

This appears to be a function of the availability of nest trees instead of a dependence on riparian forest.

Swainson’s hawks are essentially plains or open-country hunters, requiring large areas of open landscape for foraging. With substantial conversion of grasslands to farming operations, they have shifted their nesting and foraging into those agricultural lands that provide low, open vegetation and high rodent prey populations such as alfalfa fields. Threats to Swainson’s hawk include loss and fragmentation of foraging habitat, loss of nesting habitat, disturbance of nests and pesticide poisoning in wintering habitat (Anderson et al., 2007).

Potential for Occurrence in the Project Area. Swainson’s hawks are known to occur in the project site.

Suitable foraging and nesting habitat is present in and adjacent to the project area.

North Stockton
Six occurrences have been documented within the Delta Front/North Stockton project area. Two occurrences exist within the project footprint at Mosher Slough and Calaveras-Right. One occurrence exists at Calaveras-Right within 0 to 100 feet of the project area. Two occurrences exist within 101 and 500 feet from the project at Mosher Slough at Shima Tract and Calaveras-Right. Three occurrences exist within 501 feet to 0.5 miles at Shima Tract, Fourteenmile Slough Dry Land Levee and Calaveras-Right.

Central Stockton
Eight occurrences were documented. Three occurrences exist within the project footprint at SJR Mile, French Camp Slough and Duck Creek. One occurrence exists within 101 and 500 feet from the project area at Calaveras-Left. Four occurrences exist within 501 feet to 0.5 miles at Calaveras Left, SJR and Smith Canal.

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San Joaquin County, CA Affected Environment and Environmental Consequences RD 17 Area
Eight occurrences have been documented. Two occurrences are within the proposed project footprint along the SJR and additional 3 occurrences are documented for the west bank of the SJR immediately opposite the project area. The remaining 3 occurrences are east of the project area, within the interior of RD 17.

Tricolored Blackbird
Status. The tricolored blackbird (Agelaius tricolor) is a USFWS Bird of Conservation Concern and California State candidate species (December 2015). Tricolored blackbird is a medium-sized blackbird that is distinguished from other blackbirds by its distinctive white-tipped red shoulder patches on mature males.

Females show varying amounts of red on the shoulders and their plumage is sooty brown and streaked overall.

Distribution and Habitat. The species is largely endemic to California, with smaller populations in Baja, Nevada Oregon and Washington. During the breeding season, tricolored blackbirds inhabit the Central Valley, the low foothills of the Sierra Nevada and Coast Range from Shasta County south to Kern County, the coast from Sonoma County south to the Mexican border (Beedy, 1991).

Tricolored blackbirds nest in small-to-large colonies (up to 50,000 individuals). They often return to the same nesting areas in subsequent years but will occasionally relocate their breeding colonies if suitable habitat is available elsewhere. The tricolored blackbird breeds in large colonies near fresh water, preferably in emergent wetland with tall, dense cattails or tules but also in thickets of willow, blackberry and wild rose. Nesting colonies of tricolored blackbird are highly susceptible to disturbance. Ideal breeding habitat includes two elements: (1) dense nesting substrate (i.e., blackberry or aquatic emergent vegetation) which provides protection from predators; and (2) a large supply of insects within proximity to nests and occurring at the time of fledging. Tricolored blackbirds forage in large flocks and may travel up to 4 miles (6.4 km) from nest or roost sites to forage. They forage on the ground in croplands, grassy fields, flooded land and along edges of ponds (Zeiner et al., 1990). In the Delta and Central Valley, foraging habitat consists primarily of pastures and certain types of agricultural fields.

Potential for Occurrence in the Project Area. The tricolored blackbird is unlikely to occur in the project site. Foraging habitat is present in small areas of freshwater marsh and riparian habitats. However, nesting is not expected because of low-quality habitat. The tricolored blackbird is not known to occur in the North or Central Stockton reaches of the study area.

RD 17 Area
Five occurrences have been documented within the project footprint. One occurrence exists south of Howard road, 0.5 mile east of the project area. Two occurrences exist 0.5 mile west of Interstate 5 and the SJR. Two additional occurrences exist at the southern end of the project area more than 1 mile away.

Yellow-Headed Blackbird
Status. The yellow headed blackbird (Xanthocephalus xanthocephalus) is a California State Species of Special Concern. The adult male is mainly black with a yellow head and breast with a white wing patch sometimes only visible in flight. The adult female is mainly brown with a dull yellow throat and breast.

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San Joaquin County, CA Affected Environment and Environmental Consequences Distribution and Habitat. Breeds commonly, but locally, east of Cascade Range and Sierra Nevada; in Imperial and Colorado River valleys; in the Central Valley; and at selected locations in the Coast Ranges west of the Central Valley. They nest in colonies, often sharing their habitat closely with the red-winged blackbird in fresh emergent wetland with dense vegetation and deep water, often along borders of lakes or ponds. The species forages in emergent wetland and moist, open areas, especially cropland and muddy shores of lacustrine habitat. Distribution is restricted to the Central Valley in winter, occurring mainly in the western portion. Occurs as a migrant and local breeder in deserts and along the coast of Orange County.

It is known to have bred as high as 2000 m (6600 ft) in San Bernardino Mountains (Grinnell and Miller, 1944; McCaskie et al., 1979; Garrett and Dunn, 1981).

Potential for Occurrence in the Project Area. The yellow headed blackbird is unlikely to occur within the project area and there were no known occurrences in the North and Central Stockton reaches.

RD 17 Area
Three occurrences have been documented. One occurrence exists within 501 feet to 0.5 miles. Two occurrences exist within greater than 0.5 miles and less than 1 mile.

Special Status Plant Species
A total of 18 special-status plant species were evaluated for their potential to occur in the project areas. Six of these species were identified from documented CNDDB (2014) occurrences within USGS 7.5-minute quadrangle Waterloo [478C]), Lodi South [479D], Stockton East [461B], Stockton West [462A], Lathrop [462D], Manteca [461C]. A search of the USFWS endangered species database produced two special-status plant species (USFWS 2014). The 18 species consist of Alkali milk-vetch (Astragalus tener), Heartscale (Atriplex cordulata var.cordulata), San Joaquin spearscale (Atriplex joaquinana) Round leaved filaree (California macrophylla) Owl’s clover (Castilleja campestris ssp. succulent) slough thistle (Cirsium crassicaule), Big tarplant (Blepharizonia plumose), watershield (Brasenia schreberi) Palmate-bracted bird’s beak (Chloropyron palmatum), Delta button celery (Eryngium racemosum), rose mallow (Hibiscus lasiocarpus), Delta tule pea (Lathyrus jepsonii var. jepsonii), Mason’s lilaeopsis (Lilaeopsis masonii), Delta mudwort (Limosella subulata), Sanford’s arrowhead (Sagittaria sanfordii), Suisun marsh aster (Symphyotrichum lentum), Wright’s trichocoronis (Trichocoronis wrightii var. wrightii) and Saline clover (Trifolium hydrophilium). Table 5-35 lists each special-status plant species along with its regulatory, Federal, State and CNPS listing, its habitat requirements and information related to each species’ potential to occur overall project areas.

Potential for Occurrence in the Project Area. Four special-status plant species may occur within or adjacent to the project area. These 4 include Alkali milk-vetch, Slough thistle, Big tarplant and Rose mallow. The remaining 12 special-status plant species are unlikely to occur on or near the project site.

North Stockton
Three occurrences of Mason’s lilaeopsis exist within the project footprint at Shima Tract, Fivemile Slough and Fourteenmile Slough. One documented occurrence of Rose mallow exists on site at Calaveras-Right and another occurrence exists 100 feet of the project site at Calaveras-Right.

Central Stockton
One occurrence of Rose mallow exist within the project footprint occurrence exists 100 feet of the project site at the SJR. One occurrence of Alkali milk vetch exists at Smith Canal/ within 101-500 feet; however, the record is possibly extirpated. Three occurrences of Tule pea exist within the Central Stockton project ATTACHMENT D 1282
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San Joaquin County, CA Affected Environment and Environmental Consequences area. These are along the SJR and at Smith Canal; however, the records indicate that the plants are possibly extirpated.

RD 17 Area
Three occurrence of slough thistle exist within the project footprint at the SJR.

Special Status Fish Species
Special-status fish species that occur or could occur in or near the study area, as well as their likely status in the study area, are presented in Table 5-35. Critical habitat for Central Valley steelhead, green sturgeon, and delta smelt falls within the study area in the SJR system.

Chinook Salmon
Chinook salmon are anadromous fish, meaning that adults live in marine environments and return to their natal freshwater streams to spawn. Juveniles rear in freshwater for a period of up to 1 year until smoltification (i.e., a physiological preparation for survival in marine environments) and subsequent ocean residence.

Two distinct runs of Chinook salmon occur in the SJR system: fall-run and late fall–run. The runs are named after the season of adult migration. Each run has a distinct combination of adult migration, spawning, juvenile residency and smolt migration periods. In general, fall- and late fall-run Chinook salmon spawn soon after entering their natal streams.

Central Valley Fall-/Late Fall-run Chinook salmon ESU (Oncorhynchus tshawytscha) Status. On September 16, 1999 (64 FR 50393), NMFS determined that listing was not warranted for the Central Valley fall-/late fall-run Chinook salmon ESU; however, the ESU was designated as a candidate for listing because of concerns about specific risk factors. On April 14, 2004 (69 FR 19975) the Central Valley fall-/late fall-run Chinook salmon ESU was classified as a species of concern. The ESU includes all naturally spawned populations of fall-run Chinook salmon in the Sacramento and SJR Basins and their tributaries east of the Carquinez Strait. The Central Valley fall-/late fall-run Chinook salmon ESU is currently the largest run of Chinook salmon in the SJR system. Because they represent the greatest proportion of all four runs in the Central Valley, they continue to support commercial and recreational fisheries of significant economic importance.

Distribution and Habitat. Fall-run Chinook salmon adults would primarily pass through the study area on their way to spawn in tributaries of the SJR (Moyle, 2002). Juveniles migrate from SJR tributaries (e.g., Stanislaus, Merced and Tuolumne rivers) and other river tributaries, through the SJR during the late winter and spring (February through mid-June) (San Joaquin River Group Authority, 2009). Juvenile Chinook salmon utilize the edges of rivers and sloughs for rearing as they migrate downstream (Moyle, 2002).

The Central Valley fall‐/late fall–run Chinook salmon ESU includes all naturally spawned populations of fall-run Chinook salmon in the Sacramento and SJR basins and their tributaries. Central Valley fall‐/late fall–run Chinook salmon are currently the most abundant and widespread salmon runs in California (Mills et al. 1997). The average escapement in-river on the Sacramento and San Joaquin system from 1960 to 2010 was 231,009 (CDFW, 2013).

Adult fall‐run Chinook salmon migrate into the SJR and its tributaries from June through December in mature condition and spawn from late September through December, soon after arriving at their spawning grounds (Yoshiyama et al., 1998). The spawning peak occurs in October and November. Emergence occurs from December through March and juveniles migrate downstream to the ocean soon after emerging, rearing ATTACHMENT D 1283
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San Joaquin County, CA Affected Environment and Environmental Consequences in fresh water for only a few months. Smolt outmigration typically occurs from March through July (Yoshiyama et al., 1998).

Late fall-run Chinook salmon migrate upstream before they are sexually mature and hold near spawning grounds for 1 to 3 months before spawning. Upstream migration takes place from October through April and spawning occurs from late January through April, with peak spawning in February and March (Yoshiyama et al., 1998). Fry emerge from April through June. Juvenile late fall-run Chinook salmon rear in their natal streams during the summer and in some streams they remain throughout the year. Smolt outmigration can occur from November through May (Yoshiyama et al., 1998).

Potential for Occurrence in the Project Area. These fish occur in the Sacramento and SJR, tributaries and Delta. The species occurs seasonally in the SJR in the project vicinity.

Central Valley Steelhead DPS (Oncorhynchus mykiss)
Status. On March 19, 1998, NMFS listed the Central Valley steelhead DPS as threatened (63 FR 13347).

Central Valley steelhead DPS are all considered to be winter-run steelhead (McEwan and Jackson, 1996).

Similar to other anadromous salmonid species, these fish mature in the ocean before entering freshwater on their spawning migrations. The project site is located within designated critical habitat for the Central Valley DPS. The major factor influencing steelhead populations in the SJR system is the loss of habitat due to construction of impassable dams on major tributaries leading to favorable spawning areas.

Distribution and Habitat. Adult steelhead migrate upstream to spawning habitat during the winter and early spring. Females use riffles or pools with gravel substrate to spawn and then return to sea after resting in slower moving waters. Juvenile steelhead reside in nursery streams for one to three years before migrating to the ocean in the spring. Similar to Chinook salmon, juvenile steelhead would likely utilize the edges of rivers and sloughs for rearing as they migrate (Moyle, 2002).

Potential for Occurrence in the Project Area. The SJR near the project site would be used by adult and juvenile steelhead primarily as a migration corridor between the ocean and cold-water habitat in the upstream tributaries which would include the Calaveras River.

Green Sturgeon (Acipenser medirostris)
Status. On January 23, 2003, NMFS determined that green sturgeon (Acipenser medirostris) are comprised of two populations, a northern and a southern DPS (NMFS 2003). The northern DPS includes populations extending from the Eel River northward and the southern DPS includes populations south of the Eel River to the Sacramento River. The Sacramento River supports the southernmost spawning population of green sturgeon (Moyle 2002). On April 6, 2005, NMFS determined that the northern DPS does not warrant listing under the ESA, but it remains on the Species of Concern List (NMFS 2005c). On April 7, 2006, NMFS determined that the southern DPS of green sturgeon was threatened under the Federal ESA (NMFS 2006).

On October 9, 2009, NMFS (74 CFR 52300) designated critical habitat for the green sturgeon southern DPS throughout most of its occupied range.

Green sturgeon were classified as a Class 1 Species of Special Concern by CDFW in 1995 (Moyle et al. 1995). Class 1 Species of Special Concern are those that conform to the State definitions of threatened or endangered and could qualify for addition to the official list. On March 20, 2006, emergency green sturgeon regulations were put into effect by CDFW requiring a year‐round zero bag limit of green sturgeon in all areas (CDFG 2006).

Distribution and Habitat. The green sturgeon is anadromous but it is the most marine-oriented of the sturgeon species and has been found in near shore marine waters from Mexico to the Bering Sea (NMFS 2005c). The southern DPS has a single spawning population in the Sacramento River (NMFS 2005d) and ATTACHMENT D 1284
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Adults typically migrate upstream into rivers between late February and late July. Spawning occurs from March to July, with peak spawning from mid‐April to mid‐June. Green sturgeon are believed to spawn every 3 to 5 years, although recent evidence indicates that spawning may be as frequent as every 2 years (NMFS 2005c). Little is known about the specific spawning habitat preferences of green sturgeon. Adult green sturgeon are believed to broadcast their eggs in deep, fast water over large cobble substrate, where the eggs settle into the interstitial spaces (Moyle 2002). Spawning is generally associated with water temperatures from 46 to 57 degrees Fahrenheit (°F). In the Central Valley, spawning occurs in the Sacramento River upstream of Hamilton City, perhaps as far upstream as Keswick Dam (Adams et al. 2002) and the lower Feather River (Seesholtz et al. 2012).

Green sturgeon eggs hatch in about 8 days at 55°F (Moyle 2002). Larvae begin feeding 10 days after hatching. Metamorphosis to the juvenile stage is complete within 45 days of hatching. Juveniles spend 1 to 4 years in fresh and estuarine waters and then migrate to salt water at lengths of 300 to 750 millimeters (mm) (NMFS 2005c). The juvenile habitat is poorly understood. Juvenile green sturgeon inhabit the Sacramento River and Delta. In the river, they occupy low-light habitats with some rock structure during their first winter. Juveniles have been reported to forage at night while seeking the darkest available habitats during the day (Kynard 2005 in Israel and Klimley 2008). Juvenile green sturgeon have morphological and behavioral attributes for holding in flowing riverine environments (Allen et al. 2006a in Israel and Klimley 2008). In the estuary, it is possible that older juvenile green sturgeon are capable of moving across highly variable physical gradients in salinity, temperature and dissolved oxygen as are adults in the ocean environment (Kelly et al. 2007, Moser and Lindley 2007 in Israel and Klimley 2008). Kaufman et al. (2006) found the oxygen binding of green sturgeon juveniles appeared to have low temperature sensitivity that would permit fishes to bind sufficient oxygen with increased water temperatures. The oxygen binding and uploading responses of juvenile green sturgeon across a range of temperatures between 110 and 240 C suggests they are capable of inhabiting slightly hypoxic-environments while maintaining moderate aerobic activity (Kaufman et al. 2006). These experimental data also suggest green sturgeon have a limited ability to handle increased environmental C02. Flow may indirectly influence juvenile foraging and survival by modifying the availability of freshwater and low-salinity habitats in the Delta and Suisun Bay during green sturgeon’s first year of life (Israel and Klimley 2008).

Little is known about movements, habitat use and feeding habits of green sturgeon. Green sturgeon have been salvaged at the State and Federal fish collection facilities in every month, indicating that they are present in the Delta year‐round. Juveniles and adults are reported to feed on benthic invertebrates, including shrimp and amphipods and small fish (NMFS 2005c).

Potential for Occurrence in the Project Area. Information regarding green sturgeon distribution in the SJR was limited to anecdotal reports and CDFW sturgeon report card data. Information regarding sturgeon habitat use and movements throughout the SJR is lacking but critical to improve management and protection of these species. Angler fishing report cards document a small sturgeon fishery in the reach of the SJR upstream of Stockton, California (river kilometer, hereafter rkm, 64). Since implementation of the Sturgeon Report Card in 2007, anglers have reported catching 169 white sturgeon and 6 green sturgeon on the SJR upstream from Stockton (Gleason et al. 2008; DuBois et al. 2009, 2010, 2011 and 2012, as cited in Jackson, Z. J. and J. P. Van Eenennaam, 2013). Of the reported fish, 108 (64 percent) white and 5 (83 percent) green sturgeon were caught between Stockton and the Highway 140 bridge (rkm 202). The remaining 61 (36 percent) white and 1 (17 percent) green sturgeon were caught upstream of the Highway 140 bridge. Reports indicate anglers concentrate in two areas known locally as Sturgeon Bend (rkm 119) and Laird Park (rkm 143; H. Rutherford, CDFW warden, personal communication, as cited in Jackson, Z. J. and J. P. Van Eenennaam. 2013). Additionally, anglers and game wardens indicate that sturgeon caught during March ATTACHMENT D 1285
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Delta Smelt
Status. Delta smelt (Hypomesus transpacificus) was Federally-listed as threatened on March 5, 1993 (USFWS 1993). Critical habitat was designated on December 19, 1994 (USFWS 1994). Population trends and abundance of Delta smelt are poorly understood due to their short life span (1 year). Based on data from 21 years of monthly sampling in Suisun Marsh, Delta smelt appear to be experiencing long‐term declines (Matern et al. 2002). Summer tow‐net and fall/mid‐water trawl data show fluctuating annual abundance from 1991 through 1996, with an increasing trend in the late 1990s, followed by an overall decline in abundance since 1999 (Bryant and Souza 2004).

Distribution and Habitat. Delta smelt are endemic to the Sacramento-San Joaquin estuary and are found seasonally in Suisun Bay and Suisun Marsh. Historically, the upstream limits of their range were the upper limits of the Delta (Sacramento on the Sacramento River and Mossdale on the SJR). The lower limit is the western Suisun Bay (Radtke 1966; Moyle 1976, as cited in Moyle et al. 1992). Delta smelt are typically found in shallow water (less than 10 feet) where salinity ranges from 2 to 7 parts per thousand (ppt), although they have been observed at salinities between 0 and 18.4 ppt. They have relatively low fecundity.

Most live for 1 year and feed on planktonic copepods, cladocerans, amphipods and insect larva (Moyle 2002).

Delta smelt are semi‐anadromous. During their spawning migration, adults move into the freshwater channels and sloughs of the Delta between December and January. Spawning occurs between January and July, with peak spawning from April through mid‐May (Moyle 2002). Spawning locations in the Delta identified and are inferred from larval catches (Bennett 2005). Larval fish have been observed in:

Montezuma Slough; Suisun Slough in Suisun Marsh; the Napa River estuary; the Sacramento River above Rio Vista; and Cache, Lindsey, Georgiana, Prospect, Beaver, Hog, Sycamore and Barker Sloughs (Wang 1986; Moyle 2002; Stillwater Sciences 2006; and USFWS 1996). Spawning was also observed in the Sacramento River up to Garcia Bend (RM 51) during drought conditions, as a result of increased saltwater intrusion that moved Delta smelt spawning and rearing farther inland (Wang and Brown 1993).

Laboratory experiments have found eggs to be adhesive, demersal and usually attached to substrate composed of gravel, sand or other submerged material (Moyle 2002, Wang 1991). Hatching takes 9 to 13 days and larvae begin feeding 4 to 5 days later. Newly hatched larvae contain a large oil globule that makes them semi‐buoyant and allows them to stay near the bottom. As their fins and swim bladder develop, they move higher into the water column and are transported downstream to the open waters of the estuary (Moyle 2002).

Potential for Occurrence in the Project Area. Delta smelt occur in tidally influenced segments of the Sacramento and SJRs, tributaries and Delta. Has potential to occur in the SJR in the project vicinity.

Longfin Smelt
Status. Longfin smelt are designated as a Federal species of concern and listed as a threatened species under California ESA.

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San Joaquin County, CA Affected Environment and Environmental Consequences Distribution and Habitat. Distribution of longfin smelt is centered in the West Delta, Suisun Bay and San Pablo Bay. In wet years, they are distributed more toward San Pablo Bay and in dry years more toward the west Delta. Peak spawning occurs between February and April in upper Suisun Bay and the lower and middle Delta. Spawning takes place at night, in sandy substrates near rocks and aquatic plants. After spawning, most smelt will die but some females have been known to survive another year. Spawning rarely occurs upstream of Medford Island in the SJR (Moyle et al., 1995).

Potential for Occurrence in the Project Area. The study area is upstream of Medford Island and longfin smelt eggs and larvae are not expected to occur near the project.

Sacramento Splittail
Status. On September 22, 2003, USFWS removed Sacramento splittail from the list of threatened species.

At the time of delisting, the USFWS determined that threats to Sacramento splittail were being addressed through habitat restoration actions such as the CALFED Bay-Delta Program and the CVPIA. However, the delisting is currently being reviewed under court order. Sacramento splittail are endemic to California.

Except for very wet years, they are mostly confined to the Delta, Suisun Bay, Suisun Marsh and Napa Marsh (USFWS, 1996).

Distribution and Habitat. Overall, the species distribution has been reduced to less than one-third of its original range. Splittail spawn in late April and May in Suisun Marsh and between early March and May in the upper Delta and lower reaches of the Sacramento and SJRs. Spawning in the tidal freshwater habitats of the Delta has been observed as early as January and as late as July (Sommer et al., 2002). Spawning occurs primarily in the lower reaches of rivers, flood bypasses and dead-end sloughs. Eggs adhere to benthic substrates and vegetation when laid (Wang, 1986). Splittail occur in the SJR upstream of its confluence at the Tuolumne River (Moyle, 2002) with adults and juveniles having been reported upstream of Modesto (USFWS, 1996). Juvenile emigration into the Delta begins in late winter (e.g., February) and continues throughout the summer. Juvenile splittails are most abundant in water less than 6 feet deep but show considerable capacity to swim against strong river and tidal currents (Moyle, 2002). As they migrate downstream to the Delta, they tend to favor areas with abundant vegetation (Wang, 1986).

Potential for Occurrence in the Project Area. Sacramento spilittail occurs in the Sacramento and SJRs, tributaries and Delta with potential to occur in the SJR in the project vicinity.

Hardhead (Mylopharodon conocephalus)
Status. Hardhead, a relatively large cyprinid species, is listed as a California Species of Special Concern; no Federal designation has been made.

Distribution and Habitat. Although this species is widespread and abundant throughout the Sacramento River and SJR systems, recent declines in numbers have raised concern. Hardhead are typically found in low- to mid-elevation streams and reservoirs. In streams, adult hardhead tend to utilize the deepest portions of the water column, rarely moving into the upper water column, while juveniles demonstrate a preference for shallow water close to the stream banks (Moyle et al., 1995). Hardheads prefer clear, deep, calm streams with temperatures in excess of 20 C. Spawning takes place in gravel or rocky substrate in runs, riffles and pools. Larval hardheads remain under vegetation near stream or lake margins and as they mature, they into deeper water.

Potential for Occurrence in the Project Area. Hardhead are unlikely to occur in the SJR near the Study Area.

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San Joaquin County, CA Affected Environment and Environmental Consequences San Joaquin Roach (Lavinia symmetricus)
Status. The San Joaquin roach is a state species of concern.

Distribution and Habitat. The roach is generally found in small warm streams at mid-elevations with dense populations being observed in isolated pools (Leidy, 2007), but are also present under diverse conditions in cooler large streams. Spawning is temperature dependent when water exceeds 16 C in March through July (Santos et al., 2014). Large groups will spawn over small rock substrates in riffles, between rock interstices (Santos et al., 2014). Due to late spring spawning, young juveniles avoid being flushed downstream to less favorable habitat due to less chance of high flow events (Santos et al., 2014).

Potential for Occurrence in the Project Area. Not likely to occur in the SJR in the project vicinity.

River Lamprey (Lampetra ayresi)
Status. On January 27, 2003, USFWS received a petition to Federally list river lamprey in Oregon, Washington, Idaho and California as threatened or endangered under the Endangered Species Act. In 2004, the USFWS found that the petition did not provide the required information to indicate that listing the species may be warranted and, therefore, a status review was not initiated.

Distribution and Habitat. River lampreys are found from just north of Juneau, Alaska, to the San Francisco Bay in California. However, detailed information on their distribution and abundance is lacking. River lampreys are associated with large river systems such as the Fraser, Columbia, Klamath, Eel and Sacramento Rivers. River lamprey appear to be concentrated only in particular rivers and only in the lower portions of these large rivers. Little is known on the life history of river lampreys in the Sacramento-SJR systems as no studies have been done on the California populations. They are an anadromous species, spending relatively short amounts of time, 3 to 4 months, in the ocean feeding on fish. Their prey of preference is salmon and herring, attaching above the lateral line and feeding on the muscle tissue. They are known to continue feeding on the organism even after it has died (Santos et al., 2014). Migration into fresh water is thought to take place in fall with spawning occurring in winter and spring in small tributaries.

Adult lampreys create depressions in the gravel of riffle systems to deposit their eggs and die after spawning (Santos et al., 2014). Larval lampreys are known as ammocoetes and once hatched, move to silt sand back waters and bury themselves tail-first. It is assumed they spend 3-5 years in freshwater systems before metamorphosing into adults. Metamorphosis occurs over a 9 to 10 month period and afterwards they aggregate in large numbers; moving to the ocean late in the spring (Santos et al., 2014).

Potential for Occurrence in the Project Area. This species occurs in tributaries of the Sacramento and SJRs.

Not likely to occur in the SJR in the project vicinity.

Factors that Affect Abundance of Fish Species
Information relating abundance with environmental conditions is mostly available for listed fish species, especially Chinook salmon. The following section focuses on factors that have potentially affected the abundance of listed species in the Central Valley. Although not all species are discussed, anthropogenic factors that negatively affect the listed species are assumed to also affect the abundance of other native and nonnative species in similar fashion for native fishes or could provide more suitable water quality conditions and habitat features to better support nonnative fishes.

Spawning Habitat Area. Spawning habitat area could limit the production of juveniles and subsequent adult abundance of some species. Spawning habitat area for fall- and late fall–run cChinookhinook salmon, which compose more than 90 percent of the Chinook salmon returning to the Central Valley streams, has been identified as limiting their population abundance. Existing spawning habitat area has not been identified as ATTACHMENT D 1288
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San Joaquin County, CA Affected Environment and Environmental Consequences a limiting factor for the less-abundant winter-run and spring-run Chinook salmon (NMFS, 2005a, USFWS, 1996) although habitat could be limiting in some streams (e.g., Butte Creek) during years of high adult abundance.

Delta smelt spawn in fresh water at low tide on aquatic, submerged, and inshore plants and over sandy and hard bottom substrates of sloughs and shallow edges of channels in the upper Delta and Sacramento River above Rio Vista (Wang 1986, Moyle, 2002). Spawning habitat area has not been identified as a factor affecting delta smelt abundance (USFWS, 1996), but little is known about specific spawning areas and requirements in the Delta.

Rearing Habitat Area. Rearing habitat area could limit the production of juveniles and subsequent adult abundance of some species. WS (1996) has indicated rearing habitat area in Central Valley streams and rivers limits the abundance of juvenile fall-run and late fall–run Chinook salmon and juvenile steelhead.

Rearing habitat for salmonids is defined by environmental conditions such as water temperature, dissolved oxygen (DO), turbidity, substrate, water velocity, water depth, and cover (Jackson, 1992; Bjornn and Reiser, 1991; Healey, 1991). Chinook salmon also rear along the shallow vegetated edges of Delta channels (Grimaldo et al., 2000).

Environmental conditions and interactions among individuals, predators, competitors and food sources determine habitat quantity and quality and the productivity of the stream (Bjornn and Reiser, 1991). Everest and Chapman (1972) found juvenile Chinook salmon and steelhead of the same size using similar inchannel rearing area.

Rearing area varies with flow. High flow increases the area available to juvenile Chinook salmon, because they extensively use submerged terrestrial vegetation on the channel edge and the floodplain. Deeper inundation provides more overhead cover and protection from avian and terrestrial predators than shallow water (Everest and Chapman in Jackson, 1992). In broad, low-gradient rivers, change in flow can greatly increase or decrease the lateral area available to juvenile Chinook salmon, particularly in riffles and shallow glides (Jackson, 1992).

Rearing habitat for larval and early juvenile Delta smelt encompasses the lower reaches of the Sacramento River below Isleton and the SJR below Mossdale. Estuarine rearing by juveniles and adults occurs in the lower Delta and Suisun Bay. USFWS (1996) has indicated that loss of rearing habitat area would adversely affect the abundance of larval and juvenile Delta smelt. The area and quality of estuarine rearing habitat are assumed to be dependent on the downstream location of 2 ppt salinity (Moyle et al., 1992). The condition where 2 ppt salinity is located in the Delta is assumed to provide less habitat area and lower quality than the habitat provided by 2 ppt salinity located farther downstream in Suisun Bay. This geographic distribution would not always be a function of outflow and 2 ppt isohaline position. Outflow and the position of the 2 ppt isohaline may account for only about 25 percent of the annual variation in abundance indices for delta smelt (DWR and USBR, 1994).

Rearing habitat has not been identified as a limiting factor in splittail population abundance but as with spawning, a lack of sufficient seasonally flooded vegetation may be limiting population abundance and distribution (Young and Cech, 1996). Rearing habitat for splittail encompasses the Delta, Suisun Bay, Suisun Marsh, the lower Napa River, the lower Petaluma River and other parts of San Francisco Bay (Moyle, 2002). In Suisun Marsh, splittail concentrate in the dead-end sloughs that have small streams feeding into them (Daniels and Moyle, 1983; Moyle, 2002). As splittail grow, salinity tolerance increases (Young and Cech, 1996). Splittail are able to tolerate salinity concentrations as high as 29 ppt and as low as 0 ppt (Moyle, 2002).

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San Joaquin County, CA Affected Environment and Environmental Consequences Migration Habitat Conditions. The SJR and the Delta provide a migration pathway between freshwater and ocean habitats for adult and juvenile steelhead and all runs of Chinook salmon. Suitable habitat conditions during steelhead and Chinook salmon spawning runs include streamflows that provide suitable water velocities and depths that provide successful passage. Flow in the San Joaquin River and in Delta provides the necessary depth, velocity and water temperature; however, flow and environmental conditions in the Central Valley are not always at optimal levels (water temperature). In the Delta, the channel pathways affect migration of juvenile Chinook salmon. Juvenile Chinook salmon survival is lower for fish migrating through the central Delta (i.e., diverted into the Delta Cross Channel and Georgiana Slough) than for fish continuing down the Sacramento River (Newman and Rice, 1997). Similarly, juvenile Chinook salmon entering the Delta from the SJR appear to have higher survival rates if they remain in the SJR channel instead of moving into Old River and the south Delta (Brandes and McLain, 2001).

Larval and early juvenile delta smelt are transported by currents that flow downstream into the upper end of the mixing zone of the estuary where incoming saltwater mixes with outflowing fresh water (Moyle et al., 1992). Reduced flow could adversely affect transport of larvae and juveniles to rearing habitat.

Adult splittail gradually move upstream during the winter and spring to spawn. Year-class success of splittail is positively correlated with wet years, high Delta outflow and floodplain inundation (Sommer et al., 1997; Moyle, 2002). Low flow impedes access to floodplain areas that support rearing and spawning.

Water Temperature. Fish species have different responses to water temperature conditions depending on their physiological adaptations. Salmonids in general have evolved under conditions in which water temperatures need to be relatively cool. Delta smelt and splittail can tolerate warmer temperatures. In addition to species-specific thresholds, different life stages have different water temperature requirements.

Eggs and larval fish are the most sensitive to warm water temperature.

Unsuitable water temperatures for adult salmonids such as Chinook salmon and steelhead during upstream migration lead to delayed migration and the potential for lower reproduction rates. Elevated summer water temperatures in holding areas cause mortality of spring-run Chinook salmon (USFWS, 1996). Warm water temperature and low DO also increase egg and fry mortality. USFWS (1996) cited elevated water temperatures as limiting factors for fall- and late fall-run Chinook salmon.

Juvenile salmonid survival, growth and vulnerability to disease are affected by water temperature. In addition, water temperature affects prey species abundance and predator occurrence and activity. Juvenile salmonids alter their behavior depending on water temperature, including movement to take advantage of local water temperature refugia (e.g., movement into stratified pools, shaded habitat, subsurface flow) and improve feeding efficiency (e.g., movement into riffles). Water temperature in Central Valley rivers frequently exceeds the tolerance of Chinook salmon and steelhead life stages. For example, adult fall-run Chinook salmon have been observed to stop their upstream migration when water temperatures exceed 66°F (Hallock et al., 1970). For Chinook salmon eggs and larvae, survival during incubation is assumed to decline with increasing temperature between 54°F and 61°F (Myrick and Cech, 2001; Seymour 1956 in Alderice and Velsen, 1978). For juvenile Chinook salmon, survival is assumed to decline as temperature warms from 64°F to 75°F (Myrick and Cech, 2001; Rich, 1987). Relative to rearing, Chinook salmon require cooler temperatures to complete the parr-smolt transformation and maximize their saltwater survival. Successful smolt transformation is assumed to deteriorate at temperatures ranging from 63°F to 73°F (Marine 1997 in Myrick and Cech, 2001; Baker et al., 1995).

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San Joaquin County, CA Affected Environment and Environmental Consequences For steelhead, successful adult migration and holding are assumed to deteriorate as water temperature warms between 52°F and 70°F. Adult steelhead seem to be more sensitive to thermal extremes than are juveniles (NMFS, 1996; McCullough, 1999). Conditions supporting steelhead spawning and incubation are assumed to deteriorate as temperature warms between 52°F and 59°F (Myrick and Cech, 2001). Juvenile rearing success is assumed to deteriorate at water temperatures ranging from 63°F to 77°F (Raleigh et al., 1984; Myrick and Cech, 2001). Relative to rearing, smolt transformation requires cooler temperatures and successful transformation occurs at temperatures ranging from 43°F to 50°F. Juvenile steelhead, however, have been captured at Chipps Island in June and July at water temperatures exceeding 68°F (Nobriga and Cadrett, 2001). Juvenile Chinook salmon have also been observed to migrate at water temperatures warmer than expected based on laboratory experimental results (Baker, 1995).

Delta smelt and splittail populations are adapted to water temperature conditions in the Delta. Delta smelt could spawn at temperatures as high as 72°F (USFWS, 1996) and could rear and migrate at temperatures as warm as 82°F (Swanson and Cech, 1995; Young and Cech, 1996).

Entrainment. All fish species are entrained to varying degrees by the SWP and CVP Delta export facilities and many other smaller diversions in the Delta and Central Valley rivers. Fish entrainment and subsequent mortality are highly variable among species and could be a function of the size of the diversion, the location of the diversion, the behavior of the fish (Swanson et al., 2004, 2005) and other factors such as fish screens, the presence of predatory species and water temperature. Diversions that divert relatively little water from the total channel and with low approach velocities are assumed to minimize stress and protect fish from entrainment.

Diversions and Delta inflow and outflow may affect survival of Delta smelt. In water exported at the South Delta CVP and SWP export facilities, estimates of Delta smelt entrainment suggest a population decline in the early 1980s, mirroring the decline indicated by mid‐water trawl, summer tow‐net, Kodiak trawl and beach seine data (Bennett 2005). Diversions and upstream storage, including operation of the CVP and SWP, control Delta inflow and outflow during most months. Reduced Delta flow may inhibit or slow movement of larvae and juveniles to estuarine rearing habitat and into deeper and narrower channels of the Delta, resulting in lower prey availability and increased mortality from predators (Moyle 2002). Low Delta flow may also increase entrainment in diversions, including entrainment at the CVP and SWP export pumps (Moyle 2002). Additional factors affecting Delta smelt abundance include extremely high river outflow that increases entrainment at export facilities, changes in prey abundance and composition, predation by nonnative species, toxic substances, disease and loss of genetic integrity through interbreeding with the introduced Wagasaki smelt (Moyle 2002; CDFG 2000; Bennett 2005). Juvenile Chinook salmon are entrained in all months, but primarily from November through June when juveniles are migrating downstream.

Although several studies documenting entrainment at small, unscreened Delta diversions are available, few address population-level effects or accurately estimate the total loss of fish at the diversions studied (Moyle and Israel, 2005). Some diversions could in fact entrain large numbers of individuals. However, many studies report capturing mostly larval or post-larval fish, with the majority of the catch being dominated by nonnative species such as gobies, threadfin shad and striped bass (Cook and Buffaloe, 1998; Nobriga et al., 2004).

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San Joaquin County, CA Affected Environment and Environmental Consequences Contaminants. In the Sacramento and SJR basins, industrial and municipal discharge and agricultural runoff transport contaminants into rivers and streams that ultimately flow into the Delta. Principal pollutants in the Delta are agricultural chemicals and their derivatives (Herbold et al., 1992). Organophosphate insecticides, such as carbofuran, chlorpyrifos and diazinon are present throughout the Central Valley and dispersed in agricultural and urban runoff. The “first-flush” storm event or the “dormant spray” storm event is of most concern because of the higher concentration of contaminants in the runoff. In particular, diazinon and chlorpyrifos are applied to control wood-boring insects in dormant stone fruit orchards from December to February (Zamora et al., 2003).

These contaminants enter rivers in winter runoff and enter the estuary in concentrations that could be toxic to invertebrates (CALFED Bay-Delta Program, 2000). Unlike severe bioaccumulators such as organochlorine pesticides, organophosphate pesticides are typically metabolized by most invertebrates.

Some organophosphate pesticides do not bioaccumulate, while some do. In particular, diazinon has a solubility of 68.9 milligrams per liter (mg/L) at 68°F but should not bioaccumulate in aquatic organisms (Zamora et al., 2003). Chlorpyrifos is more persistent in the environment and tends to be hydrophobic to the water column. Chlorpyrifos has a lower solubility than diazinon (1.12 mg/L at 75°F) and a significant potential to bioaccumulate in aquatic organisms (Zamora et al., 2003). Because some organophosphate could accumulate in living organisms, they could become toxic to fish species, especially those life stages that remain in the system year-round and spend considerable time there during the early stages of development, such as Chinook salmon, steelhead, splittail, green sturgeon and Delta smelt.

Mercury contamination from historical mining activities is extensive on both sides of the Central Valley and occurs primarily from widely scattered hydraulic mining debris along eastside tributaries and abandoned mines and associated debris piles on the west side. These sources continue to deposit significant amounts of mercury into the Bay-Delta system. The Cosumnes River, Yolo Bypass and Sacramento River are the primary ongoing sources of mercury contamination in the Bay-Delta. Mercury occurs in several forms, including pure elemental mercury and toxic methylmercury. Mercury is mobile in aquatic systems as aqueous mercury or when attached to suspended particulate matter. Methylmercury is a significant water quality concern because small amounts can bioaccumulate in fish to levels that are toxic to humans and wildlife. In the Delta, mercury concentrations in bluegill, Sacramento sucker and largemouth bass have been found to exceed the human health standard of 0.5 part per million (ppm) by two to six times (Slotten et al., 2003).

Other contaminants of particular concern in the Bay-Delta system include high concentrations of trace elements such as selenium, copper, cadmium and chromium; however, their effects on higher trophic levels are poorly understood, in part as a result of the complex distribution of high concentrations in both time and space (Herbold et al., 1992). In general, it appears that the highest concentrations occur in areas where human activity adjacent to the bay is also the highest. Although these trace elements also occur naturally, concentrations of these trace elements have been found to be high enough to adversely affect the growth and reproduction of aquatic animals in laboratory experiments (Herbold et al., 1992).

Predation. Nonnative species cause substantial predation mortality on native species. Studies at Clifton Court Forebay estimated predator-related mortality of hatchery-reared fall-run Chinook salmon to be from about 60 percent to more than 95 percent. Although the predation contribution to mortality is uncertain, the estimated mortality suggests that striped bass and other predatory fish, primarily nonnative, pose a threat to juvenile Chinook salmon moving downstream, especially where the stream channel has been altered from natural conditions. Turbulence from water passing over dams and other structures could disorient juvenile Chinook salmon and steelhead, increasing their vulnerability to predators. Predators such as striped bass, largemouth bass and catfish also prey on Delta smelt and splittail (USFWS, 1996).

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San Joaquin County, CA Affected Environment and Environmental Consequences Food. Food availability and type affect survival of fish species. Species such as threadfin shad and wakasagi could affect Delta smelt survival through competition for food. Introduction of nonnative food organisms could also affect Delta smelt and other species’ survival. Nonnative zooplankton species are more difficult for small smelt and striped bass to capture, increasing the likelihood of larval starvation (Moyle, 2002).

Splittail feed on opossum shrimp, which in turn feed on native copepods that have shown reduced abundance, potentially attributable to the introduction of nonnative zooplankton and the Asiatic clam (Potamorcorbula amurensis). In addition, the timing and quantity of flow releases made at upstream dams that is not associated with any of the proposed alternatives affects the abundance of food in rivers, the Delta and Suisun Bay. In general, the timing of flows that simulate natural flow regimes result in higher productivity including a higher input of nutrients from channel margins and floodplain inundation and higher production when low salinity occurs in the shallows of Suisun Bay. Higher productivity also increases the availability of prey organisms for Delta smelt and other fish species.

ASSESSMENT METHODS AND BASIS OF SIGNIFICANCE
Consultation History
NMFS
USACE informally consulted with the USFWS and NMFS during the development of the LSJRFS.

Meetings and phone calls with USACE and NFMS took place to discuss the LSJRFS and the potential species affected within the study area. USACE also formally consulted with NMFS, under Section 7, and received a biological opinion with an incidental take statement for listed fish and designated critical habitat.

The biological opinion included EFH recommendations.

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San Joaquin County, CA Affected Environment and Environmental Consequences During PED phase, coordination with the resource agencies would continue in order to ensure that the LSJRFS remains in compliance with the completed Section 7 consultation. USACE would coordinate potential design refinements with USFWS and NMFS to avoid, minimize and off-set any adverse effects on listed species. Formal Section 7 consultation would be reinitiated with USFWS and NMFS if changes to the LSJRFS occurred that were noncompliant with this BO. The following list summarizes the consultation history to date:
 2013 – Initial species list obtained for the study area of the LSJRFS.  May 29-30, 2013 – USFWS, DWR and USACE environmental staff participated in a field tour of the LSJRFS area.
 2014 – Updated species list obtained.
 On June 24, 2014, the USFWS submitted a Draft FWCA Report to USACE.  July 22, 2014 – USACE, USFWS and NMFS met to discuss the study status, the LSJRFS alternatives, draft impact assessment and approaches to mitigation and conservation measures.  February 5, 2015 – An updated species list for San Joaquin County and pertinent quads were obtained from the USFWS website.
 March 2, 2015 – USACE transmitted the draft Biological Assessment (BA) to NMFS and requested comments prior to initiating informal section 7 consultation with NMFS under the ESA.  March 31, 2015 – NMFS sent correspondence to USACE requesting additional information from USACE to support the consultation.
 April 2, 2015 – USACE and NMFS met to discuss NMFS’ letter advising USACE of additional information needed to support the consultation.
 July 30, 2015 – USACE and NMFS biologists had a phone conversation to discuss potential conservation measures for the LSJRFS. Discussion centered on potential areas where conservation measures would be most effective.
 September 17, 2015 – Meeting between USACE and NMFS to discuss the LSJRFS and conservation measures for the LSJRFS.
 November 9, 2015 – NMFS receives the final BA for the LSJRFS and a request for formal section 7 consultation under the ESA from USACE for effects to threatened California Central Valley (CCV) steelhead (Oncorhynchus mykiss) distinct population segment (DPS) and the threatened southern DPS (sDPS) of the North American green sturgeon (Acipenser medirostris), their designated critical habitats and EFH described for Pacific Salmon (Oncorhynchus spp.) in Amendment 18 of the Pacific Coast Salmon Fishery Management Plan (USACE 2015).  December 10, 2015 – NMFS responds to USACE that sufficient information has been made available to initiate formal consultation under section 7 of the ESA for the LSJRFS. However, NMFS stated in its letter that it will also include effects to individuals of the threatened Central Valley (CV) spring-run Chinook salmon (O. tshawytscha) evolutionary significant unit (ESU) in light of the reintroduction of this run of fish into the waters of the SJR basin. NMFS indicated that USACE should expect that a BO will be furnished to USACE on or before March 23, 2016.

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 February 27, 2015 – USACE transmits letter and BA requesting formal consultation.  June 8, 2015 – USFWS transmits letter requesting additional information.  November 6, 2015 – USACE transmits revised BA.
 December 9, 2015 – Following review of the BA, USFWS staff request Tables E1, E2 and E3, discussed in the BA and verification that USACE is consulting on effects of the project construction, ETL compliance and operation and maintenance.  December 10, 2015 – USACE transmits email with attachment "Table E: Pre-project vegetation and vegetation lost from project implementation." USACE confirms by follow up telephone call that it is consulting on ETL compliance and operation and maintenance, to the extent known, as well as project construction.
 January 7, 2016 – USFWS staff (Steve Schoenberg) attends site visit to project area with USACE (Tanis Toland, Ryan Larson), SJAFCA (Eric Ambrizz) and consultant engineer. The descriptions of future maintenance in the project description are based on discussions at this site visit.  January 21, 2016 – USACE transmits email with an attached shapefile of the project footprint with areas, work types and other information.
 January 22, 2016 – USACE staff (Tanis Toland) inform USFWS via telephone call of project changes, namely, the Dad's Point floodwall maybe a berm and the setback mitigation area will be modified (i.e., extended south, still within reach FM_30_L).  March 18, 2016 – USFWS transmits draft BO by email attachment to USACE.  March 30, 2016 – USACE transmits consolidated team comments on draft BO.  April 18, 2016 – USFWS transmits second draft BO by email attachment to USACE.  April 22, 2016 – USACE transmits consolidated team comments on second draft BO.

During the preconstruction engineering and design phase of the project, if authorized, USACE would then do a site-specific analysis including full biological site surveys and site-specific engineering. USACE shall prepare supplements to either draft or final EISs if: (1) USACE makes substantial changes in the proposed action that are relevant to environmental concerns; or (2) there are significant new circumstances or information relevant to environmental concerns and bearing on the proposed action or its impacts. If necessary, USACE would re-initiate consultation with USFWS and NMFS to address changes.

Special Status Wildlife Species
Assessment Methods
This section evaluates the effects of the proposed alternatives on special status wildlife species in the project area. Initial evaluation determined that several species potentially occur or that suitable habitat exists.

Special-status species are defined as animals that are legally protected under the Federal ESA, California ESA or other regulations and species that are considered sufficiently rare by the scientific community to qualify for such listing. Based on the USFWS (2014) species list and CNDDB (CDFG, 2014) records search for the quadrangles overlapping the affected area, 15 special-status plant and wildlife species were identified as potentially occurring (known to or may occur) in the affected area (Table 5-35).

Borrow Sites
Specific borrow locations have not been identified for the proposed project, but it is assumed that sufficient suitable materials would be available within a 25-mile radius from the project.

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San Joaquin County, CA Affected Environment and Environmental Consequences Special status species and suitable habitat for these species that are known to occur in or near the project area are identified in Table 5-35, “Special Status Species and Critical Habitats.” A literature review and database search indicates that Federally-listed threatened or endangered species may be present within 25 miles of the project action area. The CNDDB records and literature search indicates that State listed, threatened, endangered, rare or species of special concern may also be present within 25 miles. Potential borrow sites would be situated and appropriate conservation measures implemented, to avoid effecting Federal- and State-listed species.

Basis of Significance
Adverse effects on special status species were considered significant if implementation of an alternative would:
 Result in direct or indirect reduction in growth, survival or reproductive success of species listed or proposed for listing as threatened or endangered under the Federal ESA or California ESA.  Result in direct mortality, long-term habitat loss or lowered reproductive success of Federal- or State-listed threatened or endangered animal or plant species or candidates for Federal listing.  Result in direct or indirect reduction in the growth, survival or reproductive success of substantial populations of Federal species of concern, State-listed endangered or threatened species, plant species listed by the CNPS or species of special concern or regionally important commercial or game species.
 Have an adverse effect on a species’ designated critical habitat.

Special Status Fish Species
Assessment Methods
To prepare for the analysis of the potential effects on fish species, a review of existing resource information related to the project area to evaluate whether sensitive habitats and special-status fish species are known from or could occur in the study area was conducted. The information reviewed included the following sources: an USFWS list of endangered, threatened and proposed species for the Lodi South, Waterloo, Stockton East and West, Manteca and Lathrop USGS 7.5-minute quadrangles (USFWS, 2014); Google Earth ProTM; and, published and unpublished documents and reports pertaining to the study area.

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San Joaquin County, CA Affected Environment and Environmental Consequences Basis of Significance
Populations of fish and other aquatic organisms may be reduced because of increased mortality and changes in habitat availability and suitability that affect survival, growth, migration and reproduction. In general, effects on fish populations are significant when the project causes or contributes to substantial short or long term reductions in abundance and distribution. The assessment of potential effects takes into consideration the significance of an action based on its context and its intensity, as required by NEPA. Based on Section 15065 and Appendix G of the State CEQA Guidelines, an effect is found to be significant if it:
 Has a substantial adverse effect, either directly or through habitat modifications, on any species identified as a candidate, sensitive or special status species in local or regional plans, policies or regulations or by the CDFW or USFWS;
 Interferes substantially with the movement of any native resident or migratory fish or wildlife species or with established native resident or migratory wildlife corridors or impede the use of native wildlife nursery sites;
 Substantially reduces the habitat of a fish population;  Causes a fish population to drop below self‐sustaining levels;  Threatens to eliminate an animal community;
 Reduces the number or restricts the range of a rare or endangered fish species; or  Has considerable cumulative effects when viewed with past, current and reasonably foreseeable future projects.

ALTERNATIVE 1 - NO ACTION
Special Status Wildlife Species
Under the No Action Alternative, there would be no Federal action identified. Flood events may cause possible levee failure due to seepage, slope instability, erosion and overtopping. Activity involved with flood fighting, levee protection and repair have the potential to cause harm to special status species and their critical habitats. Heavy equipment would be needed to move emergency supplies and personnel to locations along the levee system requiring emergency stabilization and repair. Flood risk is expected to continue as long as the through- and under-seepage issues remain unresolved. Adverse effects to listed species could include future loss or damage of individual species and/or their terrestrial and critical habitats.

Potential losses of habitat and individual listed species could occur.

Special Status Fish Species
Under the No Action Alternative, risk to floodplain development would increase due to pressures presented by climate change. If flood events were to occur, there is a risk of possible levee failure due to seepage, slope stability, erosion, and overtopping. The chance of overtopping events increases with the challenges faced by sea level rise. Activity involved with flood fighting, levee protection and repair has the potential to cause harm to the fish populations found in the San Joaquin River system. Heavy equipment would be needed to move emergency supplies and personnel to locations along the levee system requiring emergency stabilization and repair. Heavy equipment has the potential to destroy riparian habitat used by organisms that are potential sources of food. The chemicals, oil and fuel commonly used in this equipment has the potential to leak into the environment and into the riverine system, causing injury or death to fish populations.

It is common to use large rocks and sand bags to shore up the levee system during flood events. This action has the potential to reduce habitat used by juvenile fish for protection from predators as they move downstream. In addition, the placement of and future removal of these items will potentially result in an ATTACHMENT D 1297
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San Joaquin County, CA Affected Environment and Environmental Consequences increase in sediment introduction and turbidity which would have a negative effect on fish migration, spawning locations and success, as well as rearing habitats. Noise from all activities could cause migration patterns to change to avoidance activity, disrupting successful spawning events. Given the unpredictable nature of emergency activities, it is unlikely BMPs could be implemented to reduce negative effects to fish populations.

In the event of the levee being compromised by overtopping, seepage or loss of bank stability, there are additional risks associated with fish populations. Straying could occur, causing a portion of distinct genetic population segments of fish to be unable to reach historical spawning grounds. When flood waters recede, fish strandings are likely to take place by adults as well as juvenile fish, reducing these populations. Levee failure would allow for the introduction of pollutants into the system. Flooding in developed urban areas would introduce a number of household chemicals, oils, fuels, pharmaceuticals organic and inorganic pollutants. These substances have multiple ways of affecting fish populations, increasing risk for mortality.

Agricultural land also presents the hazard for chemical and organic materials from entering the riverine system in the event of a levee breach. The use of herbicides, pesticides and fertilizers on the soil is well known. All these chemicals have numerous ways in which they will interact in an aquatic environment, having negative impact to fish populations. Potential losses of habitat and individual listed species could occur. Depending on the size of the catastrophic event, losses to listed species and critical habitat would be significant.

ALTERNATIVE 7A
Special Status Wildlife Species
Valley Elderberry Longhorn Beetle (VELB)
Direct effects to VELB may occur if elderberry shrubs are incidentally damaged by construction personnel or equipment. Impacts may also occur if elderberry shrubs need to be transplanted because they are located in areas that cannot be avoided by construction activities. Potential impacts due to damage or transplantation include direct mortality of beetles and/or disruption of their lifecycle.

Subsequent to releasing the Draft FR/EIS/EIR, a protocol-level field survey was completed within the Alternative 7a project area. Refer to Table 5-36 for quantities by area. This survey identified 44 elderberry shrubs (28 nonriparian and 16 riparian) within the Alternative 7a project area. The surveys were conducted in accordance with the Conservation Guidelines for the Valley Elderberry Longhorn Beetle (USFWS, 1999). All elderberry shrubs with the potential to be affected by project activities were mapped and surveyed to determine the size of the stems on each shrub, location of shrubs to riparian habitat and presence of exit holes. Compensation for effects to these shrubs and the beetle are in Section 5.12.10.1.

Compensation would be based upon the USFWS guidelines, which require transplanting existing shrubs when possible and new plantings of elderberry shrubs and associative plantings to provide and maintain habitat for the elderberry longhorn beetle. With the implementation of the avoidance, minimization and compensation measures, impacts to VELB would be less than significant. However, project actions are likely to adversely affect valley elderberry longhorn beetles due to potential take during construction, primarily as a result of transplanting elderberry shrubs from the construction footprint to an area outside the project footprint or an off-site conservation area.

ATTACHMENT D 1298
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San Joaquin County, CA Affected Environment and Environmental Consequences Table 5-36: Study Area Potential Elderberry Shrubs
Alternative Area Project Area Totals
Alternative 7a North Central RD 17
Riparian 8 8 0 16
Non-Riparian 0 28 0 28
Alternative 7a Total Shrubs 44
Alternative 7b North Central RD 17
Riparian 8 6 14 28
Non-Riparian 17 14 31 62
Alternative 7b Total Shrubs 90
Alternative 8a North Central RD 17
Riparian 11 14 0 25
Non-Riparian 23 31 0 54
Alternative 8a Total Shrubs 79
Alternative 8b North Central RD 17
Riparian 11 14 14 39
Non-Riparian 23 31 31 85
Alternative 8b Total Shrubs 124
Alternative 9a North Central RD 17
Riparian 8 11 0 19
Non-Riparian 17 23 0 40
Alternative 9a Total Shrubs 59
Alternative 9b North Central RD 17
Riparian 11 11 14 36
Non-Riparian 23 23 31 77
Alternative 9b Total Shrubs 113
Giant Garter Snake (GGS)
Several areas within the Alternative 7a study area may potentially affect GGS or their habitat. Construction would occur between May 1 and October 1, during the snake’s active season to minimize impacts to the species. Compensation for effects to GGS habitat is in Section 5.12.10.1. Construction would occur above the OHW line. USFWS has recommended the avoidance and minimization measures for GGS based on BMPs shown to reduce impacts to the snake.

Additional effects to GGS could occur during the installation of the closure structure measures at Smith Canal. Installation of the control structure would require coffer dams to provide a temporarily dry work space. The coffer dams and construction equipment would temporarily create noise and could prevent river connectivity for GGS movement. With the implementation of the avoidance and minimization measures described in Section 5.12.10.1, impacts to GGS could be reduced to less than significant. The potential loss of upland habitat would be mitigated by purchasing acreage from a USFWS approved mitigation bank. The implementation of the avoidance and minimization measures would help to reduce or avoid effects on GGS and its habitat that occur within 200 feet of any construction activity. The measures are based on USFWS guidelines for restoration and standard avoidance measures.

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San Joaquin County, CA Affected Environment and Environmental Consequences Additional effects to GGS could occur during the installation of the closure structure measures at Fourteenmile Slough. The effects would be similar to those regarding the Smith Canal structure. With the implementation of the avoidance and minimization measures described in Section 5.12.10.1, temporary one-season impacts to GGS would be reduced to less than significant. Despite avoidance, minimization and compensation measures, construction and O&M activities are likely to adversely affect GGS due to permanent impacts to 12.5 acres of GGS upland habitat and 0.5 acre of aquatic habitat, as well as potential take during construction activities in aquatic and upland GGS habitat.

Swainson’s Hawks
It is estimated that 139 acres of riparian habitat used by Swainson’s hawk for roosting and nesting could be affected and 363 acres of ruderal habitat could be removed or disturbed as a result of construction activities at levees. Much of this habitat is within the Stockton urban/agricultural interface, where Swainson’s hawks nest and forage along the SJR and Calaveras River. Additional habitat for Swainson’s hawks exists within and adjacent to the Sacramento Bypass. This area is less urbanized and hawks may be more sensitive to human activities. Prior to the onset of construction, biological surveys for the presence of nesting raptors (white-tailed kites, Swainson’s hawks and Cooper’s hawks) would be conducted within 0.5 mile of the proposed construction area. If a survey determines that a nesting pair is present, USACE would coordinate with CDFW and USFWS. To avoid potential effects to nesting raptors, CDFW typically requires the avoidance of nesting sites during construction activities and/or avoiding construction during the nesting season. If construction activities are determined to be necessary during the nesting season, then an on-site biologist/monitor experienced with raptor behavior would be available to monitor the nest while construction-related activities are taking place. If raptors exhibit agitated behavior in response to construction-related activities, the biological monitor would have the authority to stop work and would consult with CDFW and USFWS to determine the best course of action necessary to avoid nest abandonment or takeof individuals. The proposed conservation measures would reduce the effects on whitetailed kites, Swainson’s hawks and Cooper’s hawks to less than significant.

Short-term Effects to Special Status Bird Species
Noise, vibration, visual and proximity-related disturbances associated with construction measures could adversely affect special status birds if they are nesting on or adjacent to the study area during construction.

Bird species that could occur within the study area include burrowing owl, White-tailed kite, Song sparrow, Least Bell’s vireo and migratory bird species. Since construction would occur between August 1 and October 31, outside of the spring nesting season, it is unlikely that nesting birds would be present. However, if individuals of these species nest during the construction period, construction disturbances could cause them to abandon their nests or young. The breeding success of these species could be reduced if disturbances reduce the ability of adults to properly care for their young. The Alternative 7a construction footprint covers a large area that contains substantial nesting habitat; therefore, potential adverse effects to nesting birds are possible and are considered significant. To reduce this impact to less than significant, mitigation measures would be implemented (See Section 5.12.10.1).

Burrowing owls could potentially exist within areas disturbed by construction activities such as levees and borrow material sites. Construction activities, including grading and excavation activities at the source material sites, could result in nesting failure, death of nestlings or loss of eggs. Effects on burrowing owls could be significant if they are present at these sites. Prior to initiation of any excavation activities at the source material sites, a preconstruction survey for burrowing owls would be completed in accordance with CDFW guidelines described in the Staff Report on Burrowing Owl Mitigation (CDFG, 2012). If no burrowing owls are located during these surveys, then effects to burrowing owls would be less than significant and no mitigation would be required. If burrowing owls are located on or immediately adjacent ATTACHMENT D 1300
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San Joaquin County, CA Affected Environment and Environmental Consequences to the site, then coordination would occur with CDFW to determine the proper measures to be implemented to ensure that burrowing owls are not impacted by the project. Potential avoidance and minimization measures that could be implemented are in Section 5.12.10.1, which would reduce impacts to this species to a less than significant level.

Short Term Effects to Special Status Bat Species
Construction activities have the potential to result in direct impacts to western red bat and the pallid bat.

Though construction activities are restricted to a localized area, tree removal or trimming could occur at the project and source material sites resulting in direct disturbance or mortality to western red bat maternity roosts. Indirect impacts to western bat maternity roosts could also occur from noise and vibration caused by construction activity nearby. Impacts to the western red bat would be considered significant; however, implementation of the mitigation measures described in Section 5.12.10.1, would reduce impacts to this species to a less than significant level.

Special Status Plant Species
Construction measures have the potential to disturb plant species that have been documented in the local area. Blooming‐period surveys of the project area were not conducted for special‐status plant species with potential to occur; surveys would occur before construction. Species that may be potentially affected are Alkali milk vetch, Big tarplant, Delta tule pea, Mason’s lilaeopsis, Rose mallow and Slough thistle. The potential for loss of individual plants is likely due to the excavation of material at the levee and material source sites.

The sponsor would retain qualified botanists to and document the presence of special status plants before project implementation. The botanists will conduct a floristic survey that follows the CDFW botanical survey guidelines. If special status plant populations are detected where construction would create unavoidable impacts, the sponsor would prepare and implement a compensatory mitigation plan in coordination with USFWS or CDFW. Such plans may include salvage, propagation, on site reintroduction in restored habitats and monitoring. Implementation of these protective measures should prevent any significant adverse impact to these special status plant species.

Loss of CNPS‐listed plant species would be regulated by CDFW if the loss is substantial and could affect the long term survival of the affected population. Because the presence and extent of any special‐status plants in the project construction area are unknown, this effect would be considered significant.

Avoidance, minimization and compensation measures would be implemented in accordance with the requirements of the Federal ESA, California ESA (Section 5.12.10.2) and other relevant regulatory requirements. Habitat would be protected in place where possible. Therefore, potential adverse effects on special-status species and on sensitive habitats would be reduced to a less than significant level.

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San Joaquin County, CA Affected Environment and Environmental Consequences Special Status Fish Species
North Stockton
Alternative 7a would include the construction of levee remediation measures to address: under and through seepage; restoration to USACE levee design criteria; erosion; geometry; removal of vegetation; seismic stability; and FRM identified for Mosher Slough, Shima Tract, Fivemile Slough, Fourteenmile Slough and Tenmile Slough.

The following significant adverse effects to native and nonnative fish species could occur:

All levee fixes proposed would follow USACE’s policies regarding vegetation on levees, which forbid all woody vegetation on the crown, slopes and within 15 feet of the waterside and landside levee toes. These zones would be maintained free of woody vegetation in perpetuity. However, subsequent to release of the Draft FR/EIS/EIR, additional investigation and coordination with the NMFS’s lead senior fisheries biologist responsible for the project area, resulted in the conclusion that the full suite of characteristics that comprise SRA are not present in Mosher, Fivemile, Fourteenmile and Tenmile sloughs and no SRA is actually present in these areas.

The proposed levee fixes would require ground-disturbing activities that potentially cause erosion and soil disturbance, subsequently resulting in sediment transport and delivery to aquatic habitats. Increases in sedimentation and turbidity have been shown to affect fish physiology, behavior and habitat. An increase in sedimentation and turbidity could occur in adjacent water bodies during earth-moving activities.

High concentrations of suspended sediment can have direct and indirect effects on fish. In general, larger fish tend to be more tolerant than smaller fish, while eggs and fry are the least tolerant. For salmonids, elevated turbidity levels have been observed to elicit several behavioral and physiological responses: gill flaring, coughing, avoidance and increase in blood sugar levels. These responses indicate some levels of stress. Stress responses are generally higher with increasing turbidity and decreasing particle size. Turbidity could reach levels associated with avoidance behavior and reduced feeding success. Migrating adult salmonids have been reported to avoid high silt loads or cease migration when such loads are unavoidable (Cordon and Kelley 1961 in Bjornn and Reiser, 1991).

Short-term increases in turbidity and suspended sediment may disrupt feeding activities or result in a temporary displacement of fish from preferred habitats. High concentrations of fine sediments reduce or eliminate much of the suitable substrate necessary for macroinvertebrate production, limiting the food available to juvenile salmonids (Meehan, 1991) and other species. Consequently, growth rates of fish could be reduced if suspended sediment and turbidity levels substantially exceed ambient levels for prolonged periods. Substantial sediment input could adversely affect the migration of migratory species.

Disturbance of soil adjacent to the shoreline along levee toes and faces would temporarily increase turbidity above natural backgrounds in the immediate vicinity of these activities, potentially affecting fish species.

It is expected that turbidity resulting from construction and maintenance activities would be intense in the vicinity of the activity, but would rapidly attenuate with time and space.

ATTACHMENT D 1302
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San Joaquin County, CA Affected Environment and Environmental Consequences The potential for adverse effects on fish from an increase in turbidity and sedimentation in adjacent waters is low for the following reasons:
 Environmental commitments, including an erosion and sediment control plan would be developed and implemented before and during construction activities and would minimize the potential for increasing sedimentation and turbidity.
 Any increases in turbidity and sedimentation as a result of program activities would be temporary and limited to small portions of the overall water body.  In-water construction would be limited to the typical construction season and during periods of low fish abundance and outside the principal spawning and migration season. Typical construction season generally corresponds to the dry season, but project area construction could occur outside the limits of the dry season, only as allowed by applicable permit conditions.  Migratory and resident fish would likely move upstream, downstream or laterally to an unaffected portion of the river in response to in-channel work and would therefore be unaffected by any increases in turbidity or sedimentation should they occur.  If present, migratory species, such as adult and juvenile salmonids, would be expected to bypass channel reaches with elevated turbidity and sediment levels because a sufficient portion of the channel’s width (i.e., zone of passage) would remain unaffected.

Construction-related short term effects on fish would include effects related to noise, vibrations, artificial light and other physical disturbances caused by heavy equipment operation. These types of physical disturbances can disrupt or delay normal activities or cause injury or mortality. The potential magnitude of effects depends on a number of factors, including the type and intensity of the disturbance, proximity of the action to the water body, timing of actions relative to the occurrence of sensitive life stages and frequency and duration of activities.

For most activities, if present, noise-related effects on fish would be limited to avoidance behavior in response to movements, noises and shadows caused by construction personnel and equipment operating in or adjacent to the water body.

However, construction-related noise levels are not expected to cause delay or adversely affect upstream or downstream migration of salmon, steelhead and other migratory species for the reasons listed below:
 Construction would be limited to the typical construction season and during periods of low abundance and outside the principal spawning and migration season. Typical construction season generally corresponds to the dry season, but construction may occur outside the limits of the dry season, only as allowed by applicable permit conditions.  Migratory and resident native and nonnative fish species would likely move upstream, downstream or laterally to an unaffected portion of the river in response to noise or disturbance and would therefore be unaffected.
 If present, migratory species, such as adult and juvenile salmonids, would be expected to bypass channel reaches with noises or disturbances because a sufficient portion of the channel’s width (i.e., zone of passage) would remain unaffected.

Noise, vibrations, and other physical disturbances can harass fish, disrupt or delay normal activities, and cause injury or mortality. In fish, the hearing structures and swim bladder and surrounding tissues are particularly vulnerable to high-pressure sounds (Popper, 2006). The type and severity of effects depends on several factors, including the intensity and characteristics of the sound, the distance of the fish from the source, the timing of actions relative to the occurrence of sensitive life stages and the frequency and duration ATTACHMENT D 1303
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San Joaquin County, CA Affected Environment and Environmental Consequences of the noise-generating activities. The range of effects potentially includes behavioral effects, physiological stress, physical injury (including hearing loss) and mortality.

Given the proposed construction activities for the Fourteenmile Slough closure structure, the effects of noise on fish would be limited primarily to avoidance behavior in response to movements, vibrations and noise caused by construction personnel and equipment operating in or adjacent to the slough. However, underwater pile-driving noise could reach levels that would be capable of fish injury or mortality. Potential exposure of adult and juvenile salmonids to pile-driving sounds would be minimized by conducting all inwater pile-driving activities during 1 construction season between July 1 and September 30, when the lowest numbers of Chinook salmon and steelhead are likely to be present in the area.

There is no formal agreement on the thresholds to be used to evaluate the potential for adverse behavioral effects from underwater pile-driving noise. NMFS and USFWS generally use 150 decibel (dB) root mean square as the threshold for behavioral effects for listed salmonids. Although no scientific support for this criterion is available, it is considered a general threshold for identifying potential behavioral responses (e.g., avoidance or alarm) that could disrupt normal activity patterns or decrease the ability of fish to avoid predators.

Juvenile fish, including green sturgeon that may be residing in the detection range of pile-driving sounds (1,100 yards), could respond in ways (e.g., leaving protective cover) that increase their vulnerability to predators.

The following measures are part of the proposed project and are intended to reduce potential adverse effects on native and nonnative fish species and their habitat.  All in water construction activities would be limited to the period of June 1 through October 31 to avoid the primary migration periods of listed salmonids.  In water pile driving would be restricted to the period of July 1 through September 30 to avoid or minimize exposure of adults and juvenile salmonids to underwater pile-driving sounds.  All pile driving would be conducted by a vibratory pile driver to minimize underwater sound levels during pile-driving operations.
 Pile driving would be conducted by barge to minimize disturbance of riparian habitat.  Conduct underwater noise monitoring during in water construction to validate noise thresholds established by agreement with CDFG, USFWS and NMFS with USACE are not exceeded.

Overwater and in water structures can alter underwater light conditions and provide potentially favorable holding conditions for adult fish, including species that prey on juvenile fishes. Permanent shading from installation of piles and other structures in the Fourteenmile Slough after the closure structure construction could increase the number of predatory fish (e.g., striped bass, largemouth bass) holding in the study area and their ability to prey on juvenile salmonids and other native and nonnative fish species.

When the closure structure on Fourteenmile Slough needs to be operated, native fish species would not have the option of passing upstream or downstream of the structure. This would not be considered a significant direct effect due to the large amount of available habitat that would still exist above and below the closure structure that can be utilized until non-operational conditions resume. Construction of this structure has the potential to disturb benthic communities from disturbance of sediment. This could disrupt food sources for certain species.

Following BMPs for construction activities described above, this would result in less than significant effects on special status aquatic species. However, direct and indirect effects would be significant and unavoidable due to the permanent closure structure on Fourteenmile Slough which could have indirect effects on native fish populations due to an increase of predatory species attracted to structure and shade ATTACHMENT D 1304
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San Joaquin County, CA Affected Environment and Environmental Consequences for hiding, increasing the predation on native fish species and the potential for entrainment during gate closure. While the impacts from proposed actions will be avoided and minimized where possible, it has been determined that the project actions may affect and are likely to adversely affect Delta smelt, Central Valley steelhead and sDPS green sturgeon. We have proposed appropriate compensation for habitat impacts that could not be addressed through avoidance, minimization and conservation measures.

Central Stockton
Construction effects would be the same as those described for the Delta Front/North Stockton Reach, except for the operation of the closure structure on Smith Canal and the removal of SRA habitat.

The Central Stockton reach would also be required to establish compliance with USACE ETL vegetation requirements, as explained in detail in Section 4.6 A total of 19,630 lf of SRA habitat located on the Calaveras River, SJR, French Camp Slough and Duck Creek would be removed. The permanent loss of the woody vegetation would result in a substantial adverse effect on riparian habitat and SRA.

Because of the numerous ways that riparian vegetation influences the stream ecosystem, the effects of altering riparian vegetation are highly variable, ranging from increased sedimentation and warmer localized stream temperature to decreased food production and habitat complexity. Removal of riparian vegetation would expose soils to erosive forces such as wind and rain and could reduce overhead and instream cover (e.g., SRA cover). The removal of riparian vegetation, large woody debris and aquatic vegetation directly affects the quantity and quality of cover for fish and aquatic invertebrates.

The loss of riparian vegetation that provides SRA cover for fish as a result of vegetation removal and maintenance activities would result in greater fragmentation of existing SRA cover. Although some of the existing SRA cover currently is fragmented. Further loss or fragmentation of SRA cover in the study area contributes to the increasing and cumulative degradation of the sensitive natural community in the Delta Front/North Stockton reach.

Because of the unique value and relative scarcity of this cover type in the Sacramento and SJR systems and because SRA cover is an essential component of fish habitat, removal of SRA cover would result in a significant effect on special-status fish such as juvenile Chinook salmon, steelhead, green sturgeon, Delta smelt and Sacramento splittail.

The various actions would result in the construction-related loss of riparian habitat. As discussed above, Riparian vegetation that supports SRA cover directly influences the quality of fish habitat, affecting cover, food, in-stream habitat complexity, stream bank stability and temperature regulation. Large woody debris usually originates from riparian trees and provides habitat complexity in aquatic environments, an essential component of fish habitat.

The existing overhead shade cover within the study area varies by location and along each waterway. The amount of SRA within the study area was calculated using aerial photography and determining which areas have overhanging vegetation and trees adjacent to the natural channel and which areas do not. Generally, greater shade cover occurs during summer when full tree canopies are present. Analysis of total lf (lf) of SRA was conducted using Google Earth ProTM for the various reaches associated with ETL compliance in the study area.

Construction effects for the Smith Canal closure structure would be the same as those described for the Fourteenmile Slough closure structure. The purpose of the closure structure would be to cut off high water levels during high flow events. Operation of the closure structure would limit the water saturation levels in Smith Canal, which would reduce the risk of levee damage during flood events. Closure structure gates would be raised (closed) during high water levels on the SJR, typically during a flood event. Due to the ATTACHMENT D 1305
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San Joaquin County, CA Affected Environment and Environmental Consequences tidal influence of the Delta region, there is the potential that these high water events could last from a few days to a few months, depending on river conditions.

The Central Stockton reach would be required to establish compliance with the Vegetation ETL. Due to SRA habitat located on the Calaveras River, SJR, Duck Creek and French Camp Slough, there would be significant direct effects by reducing the available areas for shade and possible food sources available to special status fish species present in the study area. Implementation of mitigation, including receipt of a vegetation variance, would reduce direct and indirect effects from loss of SRA habitat; however, impacts to SRA, including potential entrainment during gate closure, would remain significant and unavoidable as discussed in detail in Sections 5.9 and 5.10. While the impacts from proposed actions will be avoided and minimized where possible, it was determined that the project actions may affect and are likely to adversely affect Delta smelt, Central Valley steelhead and sDPS green sturgeon. Compensation measures are proposed for habitat impacts that could not be addressed through avoidance, minimization and conservation measures. USACE will seek opportunities during PED for onsite planting of waterside vegetation, if a variance is received, in accordance with the terms and conditions of the NMFS BO.

ALTERNATIVE 7B
Alternative 7b direct and indirect effects would be the same as described in Alternative 7a. Avoidance and minimization measures that could be implemented for construction activities (other than removal of SRA habitat) would reduce impacts to the less than significant level discussed in Section 5.12.10. Compensatory mitigation to offset the effects due to loss of SRA habitat would reduce impacts; however, impacts would remain significant and unavoidable, as discussed in Sections 5.9 and 5.10. While the impacts from proposed actions will be avoided and minimized where possible, it was determined that the project actions may affect and are likely to adversely affect Delta smelt, Central Valley steelhead and sDPS green sturgeon.

We have proposed appropriate compensation for habitat impacts that could not be addressed through avoidance, minimization and conservation measures.

Special Status Wildlife Species
Valley Elderberry Longhorn Beetle
Approximately 90 shrubs may potentially exist within the Alternative 7b study area. Refer to Table 5-36 for potential quantities by area. Compensation for effects to these shrubs and the beetle are in Section

5.12.10.1. Compensation would be based upon the USFWS guidelines which require transplanting existing shrubs when possible and new plantings of elderberry shrubs and associative plantings to provide and maintain habitat for the VELB. With the implementation of the avoidance, minimization and compensation measures, impacts to VELB would be less than significant. However, project actions are likely to adversely affect valley elderberry longhorn beetles due to potential take during construction, primarily as a result of transplanting elderberry shrubs from the construction footprint to an area outside the project footprint or an off-site conservation area.

Giant Garter Snake
No occurrences of GGS have been recorded in the RD 17 project area.

Brush Rabbit
A riparian brush rabbit preserve exists immediately adjacent to the Alternative 7b study area, specifically in RD 17 at the oxbow along the SJR. The oxbow has dense riparian vegetation on the waterside west of the proposed new levee site. Most of the waterside riparian vegetation represents potentially suitable habitat, while most of the landside vegetation is not suitable habitat because of its sparseness and ATTACHMENT D 1306
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San Joaquin County, CA Affected Environment and Environmental Consequences composition. The site is monitored and maintained by the Center for Natural Lands Management.

Construction activities could result in harm to the brush rabbit and its habitat at the oxbow site. Brush rabbits could have their movement to and from the oxbow site potentially cut off by new levee construction activities. Rabbits could run onto the construction site, causing harm or death of individuals. The Sacramento USFWS wildlife office would be consulted for proper survey and monitoring technique and avoidance measures. The implementation of the avoidance and minimization measures described in Section

5.12.10.1, would help to reduce the effects to less than significant.

Special Status Plant Species
Impacts to special status plant species would be the same as described for Alternative 7a. Avoidance, minimization and compensation measures would be implemented in accordance with the requirements of the Federal ESA, California ESA (Section 5.12.10.2) and other relevant regulatory requirements. The project would protect habitat in place where possible. Therefore, potential adverse effects on special-status species and on sensitive habitats would be reduced to a less than significant level.

Special Status Fish Species
Alternative 7b direct and indirect effects due to construction for the Delta Front/North Stockton and Central Stockton reaches would be the same as Alternative 7a, but would include levee remediation measures for RD 17. Following BMPs for construction activities described in 7a, other than removal of SRA habitat, would result in a less than significant effect for special status aquatic species. Implementation of mitigation measures would reduce direct and indirect effects from loss of SRA habitat, but impacts would remain significant and unavoidable as discussed in detail in Sections 5.9 and 5.10.

RD 17
Construction effects for the RD 17 reach would be the same as those described for the Delta Front/North Stockton Reach. The RD 17 reach would be required to establish compliance with USACE Vegetation ETL requirements through either a variance or VFZ. Due to SRA habitat located on the SJR and French Camp Slough, there would be significant direct effects by reducing the available areas for shade and possible food sources available to the existing special status fish species present in the study area. Implementation of mitigation measures would reduce direct and indirect effects from loss of SRA habitat, but impacts would remain significant and unavoidable as discussed in Sections 5.9 and 5.10. While the impacts from proposed actions will be avoided and minimized where possible, it was determined that the project actions may affect and are likely to adversely affect Delta smelt, Central Valley steelhead and sDPS green sturgeon.

We have proposed appropriate compensation for habitat impacts that could not be addressed through avoidance, minimization and conservation measures.

ALTERNATIVE 8A
Alternative 8a direct and indirect effects from construction would be the same as those described for Alternative 7a, yet would include improvements along the Stockton Diverting Canal and construction of a new levee on the east side of the north bank of French Camp Slough. This alternative would not include improvements along the SJR in RD 17. Following BMPs for construction activities described in 7a, other than removal of SRA habitat, would result in a less than significant effect for special status aquatic species.

Implementation of mitigation measures would reduce direct and indirect effects from loss of SRA habitat; however impacts would remain significant and unavoidable as discussed in Sections 5.9 and 5.10. While the impacts from proposed actions will be avoided and minimized where possible, it has been determined that the project actions may affect and are likely to adversely affect Delta smelt, Central Valley steelhead ATTACHMENT D 1307
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San Joaquin County, CA Affected Environment and Environmental Consequences and sDPS green sturgeon. We have proposed appropriate compensation for habitat impacts that could not be addressed through avoidance, minimization and conservation measures.

Special Status Wildlife Species
Valley Elderberry Longhorn Beetle
Alternative 8a would affect an estimated 79 elderberry shrubs (34 more than Alternative 7a). Compensation for effects to these shrubs and the beetle are in Section 5.12.10. Compensation would be based upon USFWS guidelines, which require transplanting existing shrubs when possible and new plantings of elderberry shrubs and associative plantings to provide and maintain habitat for the VELB. With the implementation of the avoidance, minimization and compensation measures, impacts to VELB would be less than significant, but project actions are likely to adversely affect valley elderberry longhorn beetles due to potential take during construction, primarily as a result of transplanting elderberry shrubs from the construction footprint to an area outside the footprint or an off-site conservation area.

Giant Garter Snake
Alternative 8a would have additional direct and indirect effects on GGS from the proposed Stockton Diverting Canal improvements. Within the Central Stockton area, one existing CNDDB occurrence of GGS is recorded at the Stockton Diverting Channel. The channel has upland and aquatic habitat for the GGS.

The habitat area within the Stockton Diverting Channel would be disturbed by construction for a single construction season. So, the effects from construction to GGS upland habitat would be temporary. The aquatic habitat within the channel would not be disturbed during construction. No permanent loss of GGS habitat would result from construction of the project measures. Once construction is completed, the area would be returned to the pre-construction conditions and provide similar upland habitat conditions. With the implementation of the avoidance and minimization measures described in Section 5.12.10 impacts to GGS would be reduced to less than significant. Despite avoidance, minimization and compensation measures, construction and O&M activities are likely to adversely affect GGS due to the potential take during construction activities in aquatic and upland GGS habitat.

Special Status Fish Species
The Alternative 8a direct and indirect effects due to construction for the Delta Front/North Stockton and Central Stockton reaches would be the same as those described for Alternative 7a except for an extension of levee remediation on the Calaveras River and levee remediation on the Stockton Diverting Canal.

Following BMPs for construction activities described in 7a, other than removal of SRA habitat, would result in a less than significant effect for special status aquatic species. Implementation of mitigation measures would reduce direct and indirect effects from loss of SRA habitat; however, impacts would remain significant and unavoidable as discussed in Sections 5.9 and 5.10). While the impacts from proposed actions will be avoided and minimized where possible, it has been determined that the project actions may affect and are likely to adversely affect Delta smelt, Central Valley steelhead and sDPS green sturgeon. We ATTACHMENT D 1308
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San Joaquin County, CA Affected Environment and Environmental Consequences have proposed appropriate compensation for habitat impacts that could not be addressed through avoidance, minimization and conservation measures.

ALTERNATIVE 8B
Alternative 8b direct and indirect effects from construction would be the same as Alternative 7b, yet would include improvements along the Stockton Diverting Canal and construction of a new levee on the east side of the north bank of French Camp Slough. This alternative would include improvements along the SJR in RD 17.

Special Status Wildlife Species
Valley Elderberry Longhorn Beetle
Alternative 8b would affect an estimated 124 elderberry shrubs (34 more than Alternative 7b).

Compensation for effects to these shrubs and the beetle are in Section 5.12.10. Compensation would be based upon the USFWS guidelines, which requires transplanting existing shrubs when possible and new plantings of elderberry shrubs and associative plantings to provide and maintain habitat for VELB. With the implementation of the avoidance, minimization and compensation measures, impacts to VELB would be less-than-significant, but project actions are likely to adversely affect valley elderberry longhorn beetles due to potential take during construction, primarily as a result of transplanting elderberry shrubs from the construction footprint to an area outside the project footprint or an off-site conservation area.

Special Status Plant Species
Impacts to special status plant species would be the same as Alternative 7a. Avoidance, minimization and compensation measures would be implemented in accordance with the requirements of the Federal ESA, California ESA (Section 5.12.10.2) and other relevant regulatory requirements. The project would protect habitat in place where possible. Therefore, potential adverse effects on special-status species and on sensitive habitats would be reduced to a less than significant level.

Special Status Fish Species
The Alternative 8b direct and indirect effects due to construction for the Delta Front/North Stockton and Central Stockton reaches would be the same as Alternative 7b, except the additional improvements along the Stockton Diverting Canal and construction of a new levee on the east side of the north bank of French Camp Slough. Following BMPs for construction activities described in 7b, other than removal of SRA habitat, would result in a less than significant effect for special status aquatic species. Implementation of mitigation measures would reduce direct and indirect effects from loss of SRA habitat; however, impacts would remain significant and unavoidable as discussed in Sections 5.9 and 5.10. While the impacts from proposed actions will be avoided and minimized where possible, it was determined that the project actions may affect and are likely to adversely affect Delta smelt, Central Valley steelhead and sDPS green sturgeon.

We have proposed appropriate compensation for habitat impacts that could not be addressed through avoidance, minimization and conservation measures.

ALTERNATIVE 9A
Alternative 9a direct and indirect effects from construction would be the same as Alternative 7a, yet would include improvements along the Mormon Channel Bypass. This alternative would not include improvements along the SJR in RD 17. Avoidance, minimization and compensation measures would be implemented in accordance with the requirements of the Federal ESA, California ESA (Section 5.12.10) and other relevant regulatory requirements. The project would protect habitat in place where possible.

ATTACHMENT D 1309
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San Joaquin County, CA Affected Environment and Environmental Consequences Special Status Wildlife Species
Valley Elderberry Longhorn Beetle
Alternative 9a would affect an estimated 59 elderberry shrubs (14 more than Alternatives 7a).

Compensation for effects to these shrubs and the beetle are in Section 5.12.10.1 Compensation would be based upon the USFWS guidelines, which requires transplanting existing shrubs when possible and new plantings of elderberry shrubs and associative plantings to provide and maintain habitat for VELB. With the implementation of the avoidance, minimization and compensation measures, impacts to VELB would be less than significant, but project actions are likely to adversely affect valley elderberry longhorn beetles due to potential take during construction, primarily as a result of transplanting elderberry shrubs from the construction footprint to an area outside the project footprint or an off-site conservation area.

Construction of this feature has the potential to create short term habitat loss for VELB that could be present during construction. Avoidance, minimization and compensation measures would be implemented in accordance with the requirements of the Federal ESA, California ESA (Section 5.12.10.1) and other relevant regulatory requirements. The project would protect habitat in place where possible. Therefore, potential adverse effects on VELB would be reduced to a less than significant level. However, project actions are likely to adversely affect valley elderberry longhorn beetles due to potential take during construction, primarily as a result of transplanting elderberry shrubs from the construction footprint to an area outside the project footprint or an off-site conservation area.

Special Status Plant Species
Alternative 9a direct and indirect effects due to construction for the Delta Front/North Stockton and Central Stockton reaches would be the same as those described for Alternative 7a. Avoidance, minimization and compensation measures would be implemented in accordance with the requirements of the Federal ESA, California ESA (Section 5.12.10.2) and other relevant regulatory requirements. The project would protect habitat in place where possible. Therefore, potential adverse effects on special-status species and on sensitive habitats would be reduced to a less than significant level.

Special Status Fish Species
Alternative 9a direct and indirect effects due to construction for the Delta Front/North Stockton and Central Stockton reaches would be the same as Alternative 7a. In addition, construction of the Mormon Channel Control Structure and Bypass Channel would be proposed for this alternative.

This measure consists of construction of a control structure and channel improvements to allow for up to 1,200 cfs of flood flows to be diverted down this channel. The Mormon Channel control structure includes a tainter gate that would be operated to divert water into the Mormon Channel during high water events.

The gates would likely be operated every two years or so. The amount of water and duration of diverted flows would be adjusted according to the total flows moving through the system.

A flood control bypass system like this would likely only provide a corridor for migrating adult and juvenile fish, with no habitat for spawning or protection from predators. The 1,200 cfs could potentially be enough for attraction flow for fish migration up the Mormon Channel. Fish passage facilities located at the Stockton Diverting Canal should be considered in future planning. Due to the possibility of special status fish species in the Mormon Channel after a storm event, ramping down flows in the Mormon Channel so fish can escape to the main stem SJR before getting isolated in pockets and pools once flows are no longer being released into the Mormon Channel would be implemented. Following BMPs for construction activities described, other than removal of SRA habitat, would result in less than significant effects on special status aquatic species. However, short- and long-term removal of SRA habitat associated with construction activities ATTACHMENT D 1310
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San Joaquin County, CA Affected Environment and Environmental Consequences would result in a significant and unavoidable effect. While the impacts from proposed actions will be avoided and minimized where possible, it has been determined that the project actions may affect and are likely to adversely affect Delta smelt, Central Valley steelhead and sDPS green sturgeon. Appropriate compensation for habitat impacts that could not be addressed through avoidance, minimization and conservation measures is proposed.

ALTERNATIVE 9B
Alternative 9b direct and indirect effects from construction would be the same as Alternative 7b, yet would also include improvements along the Mormon Channel Bypass and improvements along the SJR in RD 17.

The potential effects from the Mormon Channel Bypass are the same as those for Alternative 9a.

Special Status Wildlife Species
Valley Elderberry Longhorn Beetle
Alternative 9b would affect an estimated 113 elderberry shrubs (24 more than Alternatives 7b). The direct and indirect effects due to construction for the Delta Front/North Stockton, Central Stockton and RD 17 reaches would be the same as described in Alternative 7b except for an extension of levee remediation on the Calaveras River and levee remediation on the Stockton Diverting Canal. Compensation for effects to these shrubs and the beetle are in Section 5.12.10. Compensation would be based upon USFWS guidelines which require transplanting existing shrubs when possible and new plantings of elderberry shrubs and associative plantings to provide and maintain habitat for VELB. With the implementation of the avoidance, minimization and compensation measures, impacts to VELB would be less than significant. However, project actions are likely to adversely affect valley elderberry longhorn beetles due to potential take during construction, primarily as a result of transplanting elderberry shrubs from the construction footprint to an area outside the project footprint or an off-site conservation area.

Special Status Plant Species
The effects of Alternative 9b from construction and operation for the Delta Front/North Stockton, Central Stockton and RD 17 reaches would be the same as those for Alternative 7b. Avoidance, minimization and compensation measures would be implemented in accordance with the requirements of the Federal ESA, California ESA (Section 5.12.10.2) and other relevant regulatory requirements. The project would protect habitat in place where possible. Therefore, potential adverse effects on special-status species and on sensitive habitats would be reduced to a less than significant level.

Special Status Fish Species
The effects of Alternative 9b from construction and operation for the Delta Front/North Stockton, Central Stockton and RD 17 reaches would be the same as those for Alternative 7b. Following BMPs for construction activities, other than removal of SRA habitat, would result in a less than significant effect on special status aquatic species. However, short- and long-term removal of SRA habitat associated with construction activities could result in a significant and unavoidable effect. While the impacts from proposed actions will be avoided and minimized where possible, it has been determined that the project actions may affect and are likely to adversely affect Delta smelt, Central Valley steelhead and sDPS green sturgeon. We have proposed appropriate compensation for habitat impacts that could not be addressed through avoidance, minimization and conservation measures.

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San Joaquin County, CA Affected Environment and Environmental Consequences

CONSERVATION AND MITIGATION MEASURES
Conservation measures are similar for Alternatives 7a, 7b, 8a, 8b, 9a and 9b though the footprint is different for each alternative. Compensation for the loss of habitat supporting special status wildlife is based on the largest potential footprint and worst case scenario under each alternative. If design refinements are made at a later time that result in reduced impacts, compensation for the permanent loss of habitat will be coordinated with the appropriate resource agencies and adjusted accordingly.

ATTACHMENT D 1312
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San Joaquin County, CA Affected Environment and Environmental Consequences Special Status Wildlife Species
Valley Elderberry Longhorn Beetle
Avoidance and Minimization Measures – Construction Phase The following is a summary of measures based on the Conservation Guidelines for the Valley Elderberry Longhorn Beetle (USFWS, 1999a). These measures would be implemented to minimize any potential effects on VELB or their habitat, including restoration and maintenance activities, long term, protection and compensation if shrubs cannot be avoided.
 When a 100‐foot (or wider) buffer is established and maintained around elderberry shrubs, complete avoidance (i.e., no adverse effects) would be assumed.  Where encroachment on the 100‐foot buffer has been approved by USFWS, a setback of 20 feet from the dripline of each elderberry shrub would be maintained whenever possible.  Shrubs that are closer than 100 feet to any work, but outside the construction footprint (construction, ETL compliance, OMRRR) are assumed to be avoided by the application of other avoidance measures such as signage, fencing, worker education and will not be subject to transplantation or the need for offset compensation.
 During construction activities, all areas to be avoided would be fenced and flagged.  Contractors and work crews would be briefed on the need to avoid damaging elderberry shrubs and the possible penalties for not complying with these requirements.  Signs would be erected every 50 feet along the edge of the avoidance area, identifying the area as an environmentally sensitive area.
 Any damage done to the buffer area would be restored.  Buffer areas would continue to be protected after construction from adverse effects of the project, such as during maintenance actions.
 No insecticides, herbicides, fertilizers or other chemicals that might harm the beetle or its host plant would be used in the buffer areas.
 Trimming of elderberry plants may be subject to mitigation measures.  Elderberry shrubs that cannot be avoided would be transplanted to an appropriate riparian area at least 100 feet from construction activities or to an approved conservation bank.  If possible, elderberry shrubs would be transplanted during their dormant season (about November, after they have lost their leaves, through the first two weeks in February). If transplantation occurs during the growing season, increased mitigation ratios would apply.  Any areas that receive transplanted elderberry shrubs and elderberry cuttings would be protected in perpetuity.
 USACE would develop off‐site compensation areas prior to or concurrent with any take of VELB.  USACE will submit its site suitability study to USFWS for review and comment prior to implementation; and request and receive written concurrence from USFWS that the site(s) is suitable for compensation for this project prior to construction.  Management of these lands would include all measures specified in USFWS’s conservation guidelines (1999a) related to weed and litter control, fencing and the placement of signs.  Monitoring would occur for ten consecutive years or for seven non‐consecutive years over a 15‐ year period. Annual monitoring reports would be submitted to USFWS.  Off site areas would be protected in perpetuity and have a funding source for maintenance.

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San Joaquin County, CA Affected Environment and Environmental Consequences Compensation Measures – Construction Phase
In accordance with the USFWS 1999 Conservation Guidelines for the Valley Elderberry Longhorn Beetle, adverse effects to the VELB would be compensated by transplanting the affected elderberries with stems greater than 1 inch in diameter and by planting a mix of native riparian/or upland vegetation at a 2:1 and 6:1 ratio depending on the diameter size of the stems. The amount of compensation for VELB was based on preliminary surveys conducted since the Draft EIS/EIR was released for review. VELB compensation is proposed to occur in the 14 acre mitigation site that has been identified at the setback levee on Fourteenmile slough. This site would be planted with transplanted shrubs and new seedlings and associated riparian habitat, in accordance with the USFWS guidelines.

Avoidance and Minimization Measures – O&M Phase
 When a 100‐foot (or wider) buffer is established and maintained around elderberry shrubs, complete avoidance (i.e., no adverse effects) will be assumed.  Where encroachment on the 100‐foot buffer has been approved by the USFWS, a setback of 20 feet from the dripline of each elderberry shrub will be maintained whenever possible.  During maintenance activities, all areas to be avoided will be fenced and flagged.  Maintenance personnel will be briefed on the need to avoid damaging elderberry shrubs and the possible penalties for not complying with these requirements.  Dust control measures shall be implemented when O&M activities take place within 100 feet of elderberry shrubs.

Compensation Measures – Operation and Maintenance Phase If elderberry shrubs require trimming during O&M activities, the non-Federal maintaining agencies would plant 1 seedling elderberry and 2 native plants for every 10 existing elderberry shrubs trimmed during O&M. A USFWS approved off site area would be identified to receive the compensation plantings.

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San Joaquin County, CA Affected Environment and Environmental Consequences Giant Garter Snake
Avoidance and Minimization Measures – Construction Phase The following measures would be implemented to minimize effects on GGS habitat that occurs within 200 feet of any construction activity. These measures are based on USFWS guidelines for restoration and standard avoidance measures included as appendices in USFWS (1997).  Unless approved otherwise by USFWS, construction would be initiated only during the GGS active period (May 1–October 1, when they are able to move away from disturbance).  All construction personnel, including workers and contractors, will participate in a worker environmental awareness training program conducted by a USFWS‐approved biologist prior to commencement of construction activities.
 A GGS survey would be conducted 24 hours prior to construction in potential habitat. Should there be any interruption in work for greater than two weeks, a biologist would survey the project area again no later than 24 hours prior to the restart of work.
 GGS encountered during construction activities would be allowed to move away from construction activities on their own.
Movement of heavy equipment to and from the construction site would be restricted to established roadways. Stockpiling of construction materials would be restricted to designated staging areas, which would be located more than 200 feet away from GGS aquatic habitat.  GGS habitat within 200 feet of construction activities would be designated as an environmentally sensitive area and delineated with signs and high visibility fencing. Fencing will be inspected and maintained as needed daily until completion of each work section of the project. This area would be avoided by all construction personnel.
 If USACE elects to use exclusionary fencing in lieu of continuous monitoring, it will be buried at least six inches below the ground to prevent snakes from burrowing and moving under the fence and will be inspected daily.
 If a frac-out is identified, all work will stop, including the recycling of the bentonite fluid. In the event of a frac-out into w6ater, the location and extent of the frac-out will be determined and the frac-out will be monitored for 4 hours to determine whether the fluid congeals (bentonite will usually harden, effectively sealing the frac-out location).
 USFWS, NMFS, CDFW and the Regional Water Quality Control Board will be notified immediately of any spills and will be consulted regarding clean-up procedures. A Brady barrel will be onsite and used if a frac-out occurs. Containment materials, such as straw bales, also will be onsite prior to and during all operations and a vacuum truck will be on retainer and available to be operational onsite within notice of 2 hours. The site supervisor will take any necessary follow-up response actions in coordination with agency representatives. The site supervisor will coordinate the mobilization of equipment stored at staging areas (e.g., vacuum trucks) as needed.
 If the frac-out has reached the surface, any material contaminated with bentonite will be removed by hand to a depth of 1-foot, contained and properly disposed of, as required by law. The drilling contractor will be responsible for ensuring that the bentonite is either properly disposed of at an approved Class II disposal facility or properly recycled in an approved manner.  Project-related vehicles will observe a 20-mile-per-hour speed limit within construction areas, except on existing paved roads where they will adhere to the posted speed limits.

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San Joaquin County, CA Affected Environment and Environmental Consequences  Aquatic habitat for the snake that would be affected by construction will be inspected for the snake, then dewatered and maintained dry and absent of aquatic prey for 5 days before initiation of construction activities. This measure applies primarily to the ditches to be relocated west of the Delta front levee sections. If complete dewatering is not possible, USFWS will be contacted to determine what if any additional measures may be necessary to minimize effects to the snake.

Compensation Measures – Construction Phase
Compensation to off-set unavoidable effects on 12.5 acres of GGS upland habitat would be provided at a ratio of 1:1 through the purchase of credits at a mitigation bank. Compensation for permanent impacts to

0.5 acres of aquatic GGS habitat will be replaced at a 3:1 ratio through the purchase of credits at a mitigation bank.

If any GGS habitat is impacted by construction, the following measures would be implemented to compensate for the habitat loss:
 Habitat (including aquatic and upland) temporarily impacted for one season (May 1–October 1) will be restored after construction by applying appropriate erosion control techniques and replanting/seeding with appropriate native plants.
 Aquatic habitat permanently impacted will be replaced at a 3:1 ratio.  Upland habitat permanently impacted will be replaced at a 1:1 ratio.  Habitat permanently or temporarily impacted outside of the May 1-October 1 work window will be created at a 2:1 ratio.
 USACE will work to develop appropriate mitigation prior to or concurrent with any disturbance of GGS habitat. Habitat will be protected in perpetuity.

The following measures would be implemented during construction of the proposed Fourteenmile Slough and Smith Canal closure structures to reduce potential adverse effects on GGS and their habitats.  Unless approved otherwise by USFWS, construction would be initiated only during the GGS’ active period (May 1–October 1, when they are able to move away from disturbance).  Install and maintain exclusion and construction barrier fencing around suitable GGS habitat.  Prepare and implement a Stormwater Pollution Prevention Plan.  Prepare and implement a Spill Prevention, Control and Counter-Measure Plan.  Conduct preconstruction surveys and monitoring for GGS.  Provide escape ramps to and cover open trenches at the end of each work day.  Restore disturbed aquatic and upland habitat to pre-action conditions.

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San Joaquin County, CA Affected Environment and Environmental Consequences Avoidance and Minimization – O&M Phase
 O&M activities would occur between May 1 and October 1 during the snake’s active season to minimize impacts to the species.
 O&M personnel will participate in USFWS‐approved worker environmental awareness program.  A GGS survey would be conducted 24 hours prior to O&M activities in potential habitat. Should there be any interruption in work for greater than two weeks; a biologist would survey the project area again no later than 24 hours prior to the restart of work.  GGS encountered during O&M activities will be allowed to move away from on their own.  Movement of heavy equipment to and from the site will be restricted to established roadways.

Stockpiling of O&M materials will be restricted to designated staging areas, which will be located more than 200 feet away from GGS aquatic habitat.

Riparian Brush Rabbit
Compensation for effects to riparian brush rabbit habitat would consist of activities to: (1) create and restore natural habitats, (2) improve or enhance habitat quality and (3) protect and preserve in perpetuity habitat and open space. Compensation for impacts to riparian brush rabbit would be provided at a ratio of 3:1 and may include both waterside and landside riparian habitat restoration or enhancement and preservation at a USFWS-approved site, which could include one or both of the proposed habitat compensation areas described below. All potential riparian brush rabbit habitat that are affected by project implementation would be compensated accordingly.

If occupied habitat would be affected, an Incidental Take Permit will be required and a separate consultation with USFWS under the FESA and with DFG under California ESA shall be conducted. These actions shall be separate from the San Joaquin County Multi-Species Habitat Conservation and Open Space Plan (SJMSCP) and will require project-specific authorization and permitting. Specific mitigation measures shall be developed during the consultation process, including, but not limited to:
 Conducting preconstruction surveys;
 Conducting daily surveys of construction areas;
 Installing exclusion fencing to prevent brush rabbits from entering construction areas;  Allowing trapping of riparian brush rabbits at the project site in support of the USFWS captive breeding program to establish new populations in appropriate habitat;  Providing on site or off site compensatory mitigation for habitat loses.

These measures to minimize direct take in conjunction with compensation for adverse effects are anticipated to avoid a net reduction in the number of riparian brush rabbits. However, the potential loss of riparian brush rabbit population in the study area could restrict the range of this species because the RD 17 area currently contains the northernmost known extent of the population on the SJR.

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San Joaquin County, CA Affected Environment and Environmental Consequences Swainson’s Hawk
To avoid and minimize effects to Swainson’s hawk, USACE would implement the following BMP measures:

Before ground disturbance, all construction personnel would participate in a CDFG-approved worker environmental awareness program. A qualified biologist would inform all construction personnel about the life history of Swainson’s hawk and the importance of nest sites and foraging habitat.

A breeding season survey for nesting birds would be conducted for all trees and shrubs that would be removed or disturbed which are located within 500 feet (0.5 miles for Swainson’s hawk) of construction activities, including grading. Swainson’s hawk surveys would be completed during at least 2 of the following survey periods: January 1 to March 20, March 20 to April 5, April 5 to April 20 and June 10 to July 30, with no fewer than 3 surveys completed in at least 2 survey periods and with at least 1 of these surveys occurring immediately prior to project initiation (Swainson’s Hawk Technical Advisory Committee, 2000). Other migratory bird nest surveys could be conducted concurrent with Swainson’s hawk surveys with at least 1 survey to be conducted no more than 48 hours from the initiation of project activities to confirm the absence of nesting. If the biologist determines that the area surveyed does not contain any active nests, construction activities, including removal or pruning of trees and shrubs, could commence without any further mitigation.

If active nests are found, USACE would maintain a 0.25-mile buffer between construction activities and the active nest(s). In addition, a qualified biologist would be present on site during construction activities to ensure the buffer distance is adequate and the birds are not showing any signs of stress. If signs of stress that could cause nest abandonment are noted, construction activities would cease until a qualified biologist determines that fledglings have left an active nest.

Other migratory birds also have potential to nest in or adjacent to the study area and would be significantly affected by construction activities. The following BMPs would be implemented:

Tree and shrub removal and other areas scheduled for vegetation clearing, grading or other construction activities would not be conducted during the nesting season (generally February 15 through August 31 depending on the species and environmental conditions for any given year). These construction activities could affect them by removing or causing abandonment of active nests of migratory birds protected under the Migratory Bird Treaty Act (MBTA) and CFGC. Implementation of minimization and avoidance measures described below would avoid, reduce or minimize the significant effect.

To reduce the impact on Swainson’s Hawk habitat, USACE will seek a vegetation variance to allow preservation of vegetation on the waterside levee slope and levee toe, and where bank protection work is performed, the sites would be planted with vegetation and trees that will provide habitat for the hawks.

To compensate for the removal of acreage of riparian habitat supporting Swainson’s hawks and other migratory birds, replacement habitat will be created as a mitigation area. For mitigation lands within the San Joaquin and Calaveras river systems, species selected to compensate for the riparian corridor removal will be consistent with the approved list of trees, shrubs and herbaceous plants native to the system.

Additional mitigation may be planted in the expanded Mormon Channel Bypass (Old Mormon Slough) or on other lands within the Stockton area that provide similar value to those removed. Mitigation within the study area will prove to be contiguous and create habitat connectivity with wildlife migratory corridors that supports the needs of important native wildlife species without compromising the integrity of the flood control facilities. The exact location of the compensation lands in the study area would be coordinated in the design phase of the project with the sponsor and comply with the local SJMSCP objectives and goals.

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San Joaquin County, CA Affected Environment and Environmental Consequences It is assumed that sufficient lands would be available within the study area; however, if there is not sufficient land, other locations within the Stockton area would be identified and public coordination would occur.

Special Status Bird Species
USACE would conduct surveys to locate nest sites of the mentioned species in suitable breeding habitats in the spring of each construction year. Surveys would be conducted by a qualified biologist using survey methods approved by USFWS. Survey results would be submitted to USFWS before construction is initiated. If nests or young of these species are not located, construction may proceed. If nests or young are located, USACE would consult with USFWS and CDFW to determine what mitigation measures could be implemented to avoid or reduce potential disturbance-related impacts to these species. Measures could include a no-disturbance buffer zone established around the nest site. The width of the buffer zone would be determined by a qualified biologist in coordination with USFWS. No construction activities would occur within the buffer zone, which would be maintained until the young have fledged (as determined by a qualified biologist).

Burrowing Owl
Prior to initiation of any excavation activities at borrow sites, a preconstruction survey for burrowing owls would be completed in accordance with CDFW guidelines described in the Staff Report on Burrowing Owl Mitigation. If no burrowing owls are located during these surveys, then effects to burrowing owls would be less than significant and no mitigation would be required. If burrowing owls are located on or immediately adjacent to the site, then coordination would occur with CDFW to determine the proper measures that would need to be implemented to ensure that burrowing owls are not impacted by the project. Potential mitigation measures that could be implemented include:
 A CDFW-qualified biologist shall conduct appropriate surveys at and around material source sites, to determine the presence/absence of burrowing owls. At least one survey shall be conducted no more than one week prior to the onset of any construction activity.  A 250-foot buffer, within which no new activity would be permissible, would be maintained between project activities and nesting burrowing owls. This protected area would remain in effect until August 31 or at CDFW discretion, until the young owls are foraging independently.  No burrowing owls could be evicted from burrows during the nesting season (February 1 through August 31). Eviction outside the nesting season could be permitted pending evaluation of eviction plans and receipt of formal written approval from CDFW authorizing the eviction.  If accidental take (disturbance, injury or death of owls) occurs, the DFG would be notified immediately.
 Conduct mandatory worker awareness training for construction personnel.

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San Joaquin County, CA Affected Environment and Environmental Consequences Special Status Bat Species
The following measures would be implemented to reduce short term impacts to special status bat species from construction of the proposed alternatives:
 A qualified biologist would examine trees for suitable bat roosting habitat before removal or trimming. High quality features (large tree cavities, basal hollows, loose or peeling bark, larger snags, palm trees, with intact thatch, etc.) would be identified and the area around these features would be searched for bats and bat signs (guano, culled insect parts, staining, etc.). If suitable habitat and/or bat signs are detected, biologists would conduct evening visual emergence surveys from half an hour before sunset to 1 to 2 hours after sunset for a minimum of 2 nights. The survey shall be conducted no more than one week prior to the onset of any construction activity. If no bat roosts are located, no further mitigation is necessary.  If active roosting western red bats are identified within the survey area, CDFW shall be immediately notified to determine what mitigation measures could be implemented to avoid or reduce potential disturbance-related impacts to these species.

Special Status Plant Species
Before project construction, surveys for special-status plants in Table 5-35 shall be conducted by a qualified botanist at the appropriate time of year when the target species would be in flower or otherwise clearly identifiable. Surveys shall be conducted in accordance with specific guidelines described by Protocols for Surveying and Evaluating Impacts to Special Status Native Plant Populations and Natural Communities (CDFG, 2009).

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San Joaquin County, CA Affected Environment and Environmental Consequences If special-status plants are found, the following measures shall be implemented:
 Qualified botanists would survey the biological study area to document the presence of specialstatus plants before project implementation and would conduct a floristic survey that follows the CDFW botanical survey guidelines (CDFG 2009). All plant species observed would be identified to the level necessary to determine whether they qualify as special-status plants or are plant species with unusual or significant range extensions. The guidelines also require that field surveys be conducted when special-status plants that could occur in the area are evident and identifiable, generally during the reported blooming period. To account for different special-status plant identification periods, one or more series of field surveys may be required in spring and summer.

If any special‐status plants are identified during the surveys, the botanist would photograph and map locations of the plants, document the location and extent of the special-status plant population on a CNDDB Survey Form and submit the completed Survey Form to the CNDDB. The amount of compensatory mitigation required would be based on the results of these surveys.  If one or more special status plants is identified in the biological study area during preconstruction surveys, the sponsor would redesign or modify the proposed project components to avoid indirect or direct effects on special status plants wherever feasible. If special status plants cannot be avoided by redesigning projects, implementation of mitigation, (avoidance, and minimization, and compensatory) would avoid significant effects on special status plants.  If complete avoidance of special status plants is not feasible, the effects of the project on special status plants would be compensated through off site preservation at a ratio to be negotiated with the resource agencies. Suitable habitat for affected special-status plant species would be purchased in a conservation area, preserved and managed in perpetuity. Detailed information would be provided to the agencies on the location and quality of the preservation area, the feasibility of protecting and managing the area in perpetuity and the responsible parties. Other pertinent information also would be provided, to be determined through future coordination with the resource agencies.

Special Status Fish Species
See also the conservation measures and mitigation associated with SRA and riparian habitat addressed in VEGETATION (Section 5.9), WILDLIFE (Section 5.10) and the BMPs associated with constructionrelated impacts such as dust, runoff and spills addressed in WATER QUALITY (Section 5.5).

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San Joaquin County, CA Affected Environment and Environmental Consequences Avoidance and Minimization Measures – Construction Phase  Use BMPs to prevent slurry seeping out to river and require piping system on land side only.  Stockpile construction materials such as portable equipment, vehicles and supplies at designated construction staging areas and barges, exclusive of any riparian and wetlands areas.  Stockpile all liquid chemicals and supplies at a designated impermeable membrane fuel and refueling station with a 110 percent containment system.  Implement erosion control measures (BMPs) including Stormwater Pollution Prevention Program and Water Pollution Control Program that minimize soil or sediment from entering the river. Install, monitor and maintain BMPs for effectiveness throughout construction operations to minimize effects to Federally listed fish and their designated critical habitat.  Schedule construction when listed terrestrial and aquatic species would be least likely to occur in the project area. If construction needs to extend into the timeframe that species are present, coordinate with the resource agencies.
 Limit site access to the smallest area possible in order to minimize disturbance.  Remove litter, debris, unused materials, equipment and supplies from the project area daily. Deposit such materials or waste at an appropriate disposal or storage site.  Immediately (within 24 hours) clean up and report any spills of hazardous materials to the resource agencies. Report any such spills and the success of the efforts to clean them up, in post‐construction compliance reports.
 Designate a USACE-appointed representative as the point-of-contact for any contractor who might incidentally take a living or find a dead, injured or entrapped, threatened or endangered species.

Identify this representative to the employees and contractors during an all employee education program conducted by USACE.
 Screen any water pump intakes, as specified by NMFS and USFWS screening specifications. Water pumps will maintain flows to keep approach velocity at the pump screens at 0.2 feet per second or less when working in areas that may support delta smelt or juvenile salmonids.

The following measures would be implemented during construction of the proposed Fourteenmile Slough and Smith Canal closure structures to reduce potential adverse effects on ESA listed species, other native fish species and their habitats.
 All in-water construction activities would be limited to the period of June 1 through October 31 to avoid the primary migration periods of listed salmonids.  In-water pile driving would be restricted to July 1 through September 30 to avoid or minimize exposure of adults and juvenile salmonids to underwater pile-driving sounds.  All pile driving would be conducted by a vibratory pile driver to minimize underwater sound levels during pile-driving operations.
 Pile driving would be conducted by barge to minimize disturbance of riparian habitat.  Conduct underwater noise monitoring during in-water construction to validate established noise thresholds are not exceeded (agreement with CDFG, USFWS, and NMFS).

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San Joaquin County, CA Affected Environment and Environmental Consequences Additional Minimization and Conservation Measures
To further avoid and minimize project effects on listed species and their critical habitat USACE would pursue the following additional measures during PED and prior to construction:
 Where suitable, pursue a vegetation variance that would allow woody vegetation to remain on the lower waterside portion of the levee and within the 15’ waterside vegetation-free zone (where removal is not otherwise required for construction of the levee improvements, floodwall or closure structures).
 USACE will seek opportunities during the design phase of the project to establish SRA compensatory mitigation if a vegetation variance is approved.  Compensation for the permanent loss of 19,630 lf of SRA would occur through the purchase of credits at a mitigation bank, if onsite mitigation is not feasible.  Minimize vegetation removal to the extent feasible.
 Minimize, to the extent possible, grubbing and contouring activities.  Identify all habitats containing or with a substantial possibility of containing, listed terrestrial, wetland and plant species in the potentially affected project areas. To the extent practicable efforts will be made to minimize effects by modifying engineering design to avoid potential direct and indirect effects.
 Incorporate sensitive habitat information into project bid specifications.  Incorporate requirements for contractors to avoid identified sensitive habitats into project bid specifications.

SOCIOECONOMICS AND ENVIRONMENTAL JUSTICE
This section describes the affected environment and environmental consequences relating to socioeconomics and environmental justice as well as the significance of the impacts and mitigation measures to reduce impacts.

ENVIRONMENTAL SETTING
Regulatory Framework
The assessment of socioeconomic resources is guided primarily by Federal laws and policies, while State and local plans and policies, including local general plan housing elements, typically promote economic development and diversity, public health and safety, housing and other concerns of the communities and resident within their jurisdictions. Environmental justice issues are mandated and regulated primarily at the Federal level. The major regulations concerning socioeconomic resources and environmental justice relevant to the proposed action are described below.

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 Executive Order 12898: Environmental Justice
 Uniform Relocation Assistance and Real Property Acquisition Policies Act State
 California Code Chapter 16: Relocation Assistance
Local
 City of Lathrop General Plan (2004)
 City of Stockton General Plan (2007)
 San Joaquin County General Plan (2007)
 City of Manteca General Plan (2013)
Environmental Justice
EO 12898, Environmental Justice, was issued in 1994. Objectives of the EO, as it pertains to this assessment, include development of Federal agency implementation strategies and identification of minority and low-income populations where proposed Federal actions have disproportionately high and adverse human health and environmental effects.

Minority populations are those persons who identify themselves as Black or African American, Hispanic, Asian American, American Indian/Alaskan Native or Pacific Islander. A minority population exists where the percentage of minorities in an affected area either exceeds 50 percent or is meaningfully greater than in the general population. Low-income populations as of 2010 are those whose income are $22,050 for a family of four and are identified using the Census Bureau’s statistical poverty threshold. USCB defines a “poverty area” as a Census tract with 20 percent or more of its residents below the poverty threshold and an “extreme poverty area” as one with 40 percent or more below the poverty level. This is significant because the social and economic welfare of minority and low-income populations may be positively or disproportionately impacted by the proposed action alternatives and because of public concerns regarding the fair and equitable treatment (meaningful involvement) of all people with respect to environmental and human health consequences of Federal laws, regulations, policies and actions.

Existing Conditions
The first two areas of concern in the study area, central and north Stockton, are located in what the U.S.

Census Bureau (USCB) refers to as the Stockton Subdivision. The third area, RD 17, is located in both the Stockton Subdivision and the Manteca Subdivision. Stockton is the seat of San Joaquin County, one of the richest agricultural and dairy regions in California. The region is the top statewide producer of asparagus and also supports a growing wine industry. Historically, Stockton’s agricultural economy has diversified to include industrial and manufacturing operations, including sulfur production. With its proximity to Interstate 5, other major highways and two transcontinental rail lines, the Port of Stockton is a major economic hub and the only port facility in California whose export tonnage exceeded import tonnage in 2011. For comparison, Table 5-37 shows the same demographic information for the State of California, San Joaquin County and the Cities of Stockton, Lathrop and Manteca.

The following analysis is based on Environmental Justice, Guidance Under the National Environmental Policy Act, prepared by CEQ and the Executive Office of the President (CEQ 1997). Although none of the published guidelines define the term “disproportionately high and adverse,” CEQ includes a nonATTACHMENT D 1324 Lower San Joaquin River
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San Joaquin County, CA Affected Environment and Environmental Consequences quantitative definition stating that an effect is disproportionate if it appreciably exceeds the risk or benefit rate to the general population.

Under the CEQ guidelines, the first step in conducting an environmental justice analysis is to determine the presence of minority and low-income populations. The second step requires that the Federal agency determine if the Federal action would result in disproportionately high or adverse health or environmental effects. The CEQ guidance indicates that when determining whether the effects are high and adverse, agencies are to consider whether the risks or rates of impact “are significant (as employed by NEPA) or above generally accepted norms.” The environmental justice analysis is based on a review of relevant demographic data to define the relative proportion of minority and low-income populations in Stockton and RD 17 (Lathrop and Manteca) to determine whether the LSJR Project would result in environmental justice effects on the relevant populations.

This section compiles demographic data on income and minority status for Stockton, Lathrop and Manteca and compares this data with the demographic profiles of San Joaquin County and California to determine if Stockton, Lathrop and Manteca contain significant minority or low-income populations.

San Joaquin County
Demographics
Approximately 78 percent of the San Joaquin County population resides in cities, 43 percent in Stockton.

The majority of San Joaquin County’s population growth between the years 2000 and 2008 occurred in incorporated areas, particularly the Cities of Lathrop, Ripon, Tracy and Manteca (AECOM, 2011:3.3-8).

Stockton, Lathrop and Manteca are within the study area.

According to the 2010 Census, San Joaquin County has a population of 685,306. San Joaquin county’s population has 68.4 percent white alone, 8.2 percent Black or African American, 2 percent American Indian and Alaska Native, 15.7 percent Asian, 0.7 Native Hawaiian and other Pacific Islander, 39.7 percent Hispanic or Latino and the remaining 5 percent classified as other or more than one ethnic group. The per capita income in San Joaquin County is $31,624 and the average salary per worker is $48,807. There are

17.5 percent of the people below the poverty level, which is more than the statewide average of 15.3 percent and less than the poverty threshold. The San Joaquin economy is more diverse, primarily as a result of its proximity to Sacramento County and the Bay Area.

Between 2006 and 2011, the population of San Joaquin County grew at an annual average rate of 1.0 percent. This growth is almost entirely due to the natural increase, as net migration ground to a halt.

However, net migration is expected to increase over the next few years as job growth attracts new residents.

The projected annual population growth in the 2012 to 2017 period averages 1.7 percent per year. The majority of the population is located in the city of Stockton with 291,707 residents. Manteca and Lathrop are two other major cities associated with the project and have 66,451 and 17,429 residents respectively.

As mentioned earlier, Stockton has the highest percentage of its population below the poverty level out of all the other cities in San Joaquin County.

Housing
Since 2007, the San Joaquin County Housing market changed. Prices dropped and the foreclosure rate leads the country. As of September 2008, the California Association of Realtors reports that the median home price dropped from the 2006 high of $250,000 to $190,000 (SJCOG) (AECOM, 2011:3.3-9).

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San Joaquin County, CA Affected Environment and Environmental Consequences Local Economy
San Joaquin County is the northernmost county in the San Joaquin Valley. Stockton is the key urban center.

The County is located in Northern California’s growth corridor. It is increasingly linked to the San Francisco Bay Area by virtue of its location and re-location of workers and companies (SJC 2010:24).

Among the county’s most important assets are the Stockton Airport and the Port of Stockton.

Agriculture was historically the County’s main economic sector and remains a basic industry. Between 1970 and 2000, direct agricultural employment in the Valley dropped from 15 percent of the total to only

8.4 percent, while agricultural services employment quadrupled (SJC, 2010:25). Growth in agricultural services employment was mainly due to high value crops, like wine, walnuts and almonds (SJC, 2010:25).

In 2007, farm production exceeded $2 billion (SJCCOG, 2008:1). Other large economic sectors in the county include transportation, warehousing, professional services and wholesale and retail trade.

Stockton
Stockton is the largest city in San Joaquin County and also the 13th largest city in California. According to the 2010 Census, Stockton’s population is made of 37 percent white alone, 12.2 percent Black or African American, 1.1 percent American Indian American Indian and Alaska Native, 21.5 percent Asian, 0.6 Native Hawaiian and other Pacific Islander, 40.3 percent Hispanic or Latino and the remaining 6.9 percent classified as other or more than one ethnic group. More than 50 percent of the population in Stockton are minorities and has 23.3 percent of the population living below the poverty line. Additionally, important information on the population’s location shows that 285,973 people (98 percent of the population) lived in households, 3,896 (1.3 percent) lived in non-institutionalized group quarters and 1,838 (0.6 percent) were institutionalized.

The median sales price for a home in Stockton in 2011 was $157,000 compared to the statewide median of $355,600. The median household income for Stockton in 2011 was $44,310 and $57,287 for the California.

The Stockton population density is 4,504.96 residents per square mile, much higher than the national average density of 81.32 residents per square mile. The population growth is much higher than the State average of 9.99 percent and is slightly higher than the National average of 9.71 percent.

On June 28, 2012, the City of Stockton filed a petition for Chapter 9 Bankruptcy protections with the United States Bankruptcy Court in Sacramento, California. The majority of the city’s budget is not impacted by the fiscal crisis. The total budget of $521 million includes $361 million in restricted funds, which cannot be used to resolve the General Fund Crisis. The $160 million General Fund provides for services such as police, fire, libraries, parks maintenance and administrative functions. These essential services would be protected for safety and welfare. The construction of setback and improvement of existing levees would not have any adverse effect on any particular group, but protect all within the floodplain equally. And since DWR and SJAFCA would be the non-Federal cost sharing partners for the project, the levee improvements would not have any significant economic effect on the population.

Lathrop
Lathrop is located in San Joaquin County, California. According to the 2010 Census data, the total Lathrop population is 18,023, which has grown 72.55 percent since 2000. The city has 21.93 square miles of land area and 1.10 square miles of water area. Lathrop population is 41.1 percent white alone, 7.2 percent Black or African American, 1.3 percent American Indian American Indian and Alaska Native, 22 percent Asian,

0.8 Native Hawaiian and other Pacific Islander, 42.6 percent Hispanic or Latino and the remaining 6.9 percent classified as other or more than one ethnic group. Lathrop only has 7.4 percent of the population below the poverty line.

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San Joaquin County, CA Affected Environment and Environmental Consequences Lathrop median household income is $62,255 in 2008-2012 and has grown by 13.11 percent since 2000.

The income growth rate is much lower than the state average of 29.28 percent and is much lower than the national average of 26.32 percent. It has a median house value of $199,400 in 2008-2012. The house value growth rate is much lower than the State average of 81.51 percent and is much lower than the National average rate of 51.67 percent.

Manteca
As of 2010, the total Manteca population is approximately 67,096. The population is 32.4 percent white alone, 4.3 percent Black or African American, 1.1 percent American Indian and Alaska Native, 7.1 percent Asian, 0.6 Native Hawaiian and other Pacific Islander, 37.7 percent Hispanic or Latino and the remaining

7.2 percent classified as other or more than one ethnic group. Manteca has 9.7 percent of the population below the poverty line.

Manteca median household income was $62,411 from 2008 to 2012. The income growth rate is higher than the State and National averages. Average house value is $225,700, up 44.59 percent since 2000.

Table 5-37: Race/Origin Characteristics and Poverty Status by City/County/State, 2010 (Percent) Race Origin
City of
Stockton
City of
Lathrop
City of
Manteca
San Joaquin
County
State of
California
Race
White 37.0 41.1 32.4 68.4 73.7
Black or African
American

12.2 7.2 4.3 8,2 6.6
American Indian and
Alaska Native

1.1 1.3 1.1 2.0 1.7
Asian 21.5 22.0 7.1 15.7 13.9
Native Hawaiian, other
Pacific Islander

0.6 0.8 0.6 0.7 0.5
Two or more ethnicities 6.9 6.9 7.2 5.0 3.6
Origin
Hispanic 40.3 42.6 37.7 39.7 38.2
Population Below Poverty Line
Percent of Total
Population

23.3 7.4 9.7 17.5 15.3
Source: USCB 2010 and ACS 5-Year Estimates, 2008-2012.

ASSESSMENT METHODS AND BASIS OF SIGNIFICANCE
Assessment Methods
This evaluation of socioeconomics and environmental justice is based on professional standards and information cited throughout the section. NEPA and CEQA requirements of social and economic effects are somewhat different. NEPA requires social and environmental analysis of a proposed project’s potential impacts on population growth and housing supply, but social and economic changes are not considered environmental impacts in and of themselves. CEQA, however, does allow discussion of social and economic changes that would result from a change in the physical environment and could in turn lead to additional changes in the physical environment (CEQ Guidelines Sec. 15064[f]).

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San Joaquin County, CA Affected Environment and Environmental Consequences The key effects were identified and evaluated based on the environmental characteristics of the LSJR project area and the magnitude, intensity and duration of activities related to the construction and operation of this project.

Basis of Significance
Implementation of a project alternative would have a significant impact with regard to population, housing and employment if it would:

Induce substantial unplanned population growth in an area, either directly or indirectly;  Result in a disproportionate effect on minority or low income communities;  Substantial change in employment;
 Displace substantial numbers of existing housing, necessitating the construction of replacement housing elsewhere;
 Displace substantial numbers of people, necessitating the construction of replacement housing elsewhere; or
 Physically divide an established community.

Implementation of a project alternative would have a significant impact with regard to environmental justice if it would have substantial and disproportionate adverse effects on the social and economic welfare of minority or low-income populations. A potential disproportionate impact may occur when the percent of minorities in the affected project area exceeds 50 percent and/or the percent of low-income exceeds 20 percent of the population or meaningfully greater than those in California. The 2010 census data indicated that the State of California, San Joaquin County and the Cities of Lathrop and Manteca all had less than 20 percent of the population below the poverty level. Furthermore, the poverty rate in Stockton is 23.3 percent, qualifying it for the USCB definition of a “poverty area.” Stockton also has a higher percentage of minorities relative to the State of California and San Joaquin County (Table 5-37).

Effects and Mitigation Measures
ALTERNATIVE 1 - NO ACTION
Under the No Action Alternative, the FRM project would not be implemented. The current level of risk would remain for a major levee failure and flooding of areas within north and central Stockton and RD 17.

Depending on the location and severity of the levee failure and duration of flooding, the location and extent of damage and impacts on existing residential, commercial, industrial and agricultural structures behind the existing levees could be from minor to extensive. Levee failure and subsequent inundation would have the potential to cut off access to certain portions of the affected communities. Levee failure and subsequent inundation would require temporary or permanent relocation of residents and businesses to nearby communities. Figures 5-7 and 5-8 show estimated flood depths in the study area in the event of a levee failure.

Under the No Action Alternative, none of the proposed flood risk reduction improvements would be implemented. The Stockton General Plan anticipates continued growth within Stockton’s sphere of influence (SOI) and planning area (Figure 5-15) with the development of a mixture of commercial, residential and public spaces suitable for local residents through planned zoning and extension of services and establishes guidelines and regulations to minimize the impacts of growth on human and environmental resources. Flooding would continue to result in short term and minor restrictions of connectivity between rural and urban areas; however, the current risk of flooding, as represented by conditions in the study ATTACHMENT D 1328
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San Joaquin County, CA Affected Environment and Environmental Consequences analysis area, would continue to pose a threat to both residents and property in and near the Cities of Stockton, Lathrop and Manteca.

A flood event could have severe consequences for agriculture and land use in the study area, thereby affecting economic productivity. Flooding could result in substantial damage to private and public property, loss of personal income and loss of public tax revenue. An estimated 235,000 residents and $28.7 billion in damageable property would continue to be at risk of unexpected levee failure and flooding in the study area. Flooding under the No Action Alternative would displace housing and people, necessitating the construction of replacement housing. Further, because Stockton, Lathrop and San Joaquin County are more than 50 percent populated by minorities and the poverty rate is more than 20 percent in Stockton; adverse effects on the economic welfare of the community would essentially affect the low income and minority population.

This has the potential to be a significant and unavoidable impact; however since the potential timing of these events and location of levee breaches cannot be predicted, this impact is likely too speculative for meaningful consideration based on available information.

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San Joaquin County, CA Affected Environment and Environmental Consequences ALTERNATIVES 7A, 8A AND 9A
Alternatives 7a, 8a and 9a consist primarily of improving existing levees in north and central Stockton, constructing two floodgates, one in Fourteenmile Slough and one at Smith Canal and constructing a flood wall at the entrance to Smith Canal at Dad’s Point. Alternative 9a also includes a flood bypass through Old Mormon Slough, which is located in central Stockton. Construction, operation and maintenance of these components of the three alternatives would result in temporary and permanent impacts on properties immediately adjacent to the levees, gates and the flood wall at Dad’s Point. These impacts would be significant because they could adversely impact occupants and the value of individual properties or neighborhoods that are directly and permanently affected by changes in the levee footprint and/or easement.

Impacts would be reduced to less than significant with mitigation. Mitigation measures are identified in Section 5.13.6.

All three alternatives would provide the same level of flood risk reduction to north Stockton. Alternative 8a would significantly reduce flood risk to all of central Stockton. Alternative 9a would reduce flood risk to all of central Stockton but would provide somewhat less risk reduction to portions that are near the Stockton Diverting Canal. Alternative 7a would reduce flood risk to all of central Stockton, but to a lesser degree than either Alternative 8a or Alternative 9a. By reducing the risk of flooding, the project would result in positive impacts to socioeconomics by reducing the likelihood of flooding, loss of lives, pain and suffering. The project would also reduce the cost of flood insurance to structures removed from the 100- year FEMA floodplain. Alternatives 7a, 8a and 9a would be an overall beneficial impact to local and regional socioeconomics.

Alternatives 7a, 8a and 9a would all reduce flood risk to the city of Stockton. Stockton has a higher percentage of minorities relative to the State of California and any other city in San Joaquin County. It also has large number of households living below the poverty line. None of these alternatives would create new barriers that would divide any established community or disproportionately impact minority or low income populations. The FRM project would benefit all residents in north and central Stockton in that it would reduce flood risk.

Alternatives 7a, 8a and 9a would not address flood risk in RD 17. Because Lathrop (located in RD 17) is more than 50 percent populated by minorities, adverse effects on the economic welfare of the community would essentially affect a minority population. This would leave Alternative 1 - No Action impacts in effect.

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San Joaquin County, CA Affected Environment and Environmental Consequences Figure 5-15: 2035 General Plan Land Use/Circulation Diagram ATTACHMENT D 1331
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San Joaquin County, CA Affected Environment and Environmental Consequences ALTERNATIVES 7B, 8B AND 9B
Alternatives 7b, 8b, 9b include the same levee improvements and gates, floodwall and flood bypass (9a and 9b only) as are described for Alternatives 7a, 8a and 9a, above. However, in addition the “b” alternatives include levee improvements to the northern, western and southern levees in RD 17 and construction of a new levee extension in the southern part of the RD 17. The improvements in RD 17 would be the same for Alternatives 7b, 8b and 9b. Construction, operation and maintenance of these alternatives would impact some properties immediately adjacent to the levees, gates and the flood wall at Dad’s Point. These impacts would be significant because they could adversely impact occupants and the value of individual properties or neighborhoods that are directly and permanently affected by changes in the levee footprint and/or easement. These impacts would be less than significant with mitigation.

None of these alternatives would create new barriers that would divide any established community, displace existing housing or displace people, and would not disproportionately impact minority or low income populations.

Alternatives 7b, 8b and 9b would reduce flood risk to residents and businesses in north and central Stockton and in RD 17, including the Cities of Manteca and Lathrop. Residents in these areas would be removed from the 100-year FEMA floodplain and, therefore, would benefit over the long-term from reduced flood insurance costs. By reducing flood risk to RD 17, barriers to implementing planned development would be removed. In addition, lands currently in agriculture and open space would become subject to increased development pressure. Conversion of agricultural and open space lands to urban uses would be a beneficial impact to socioeconomics to the extent that it permitted implementation of approved land use plans. This would produce an overall beneficial impact to local and regional socioeconomics.

Alternatives 7b, 8b and 9b would all reduce flood risk to the Cities of Stockton, Lathrop and Manteca.

Stockton has a higher percentage of minorities relative to the State of California and any other city in San Joaquin County. It also has large number of households living below the poverty line. Lathrop is more than 50 percent populated by minorities. None of these alternatives would create new barriers that would divide any established community or disproportionately impact minority or low income populations. The FRM project would benefit all residents in Stockton and in RD 17, including Lathrop and Manteca, in that it would reduce their flood risk.

MITIGATION
Project planning for all of the action alternatives has included attention to avoiding and minimizing potential impacts to adjacent properties to the extent feasible in consideration of the FRM goals of the study. Potential significant adverse impacts to adjacent properties would be mitigated through appropriate compensation. If relocation of people or their homes are required, they would be compensated under the Federal Relocation Act. With mitigation, the potentially significant impacts to adjacent property owners of implementing Alternatives 7a, 8a, 9a, 7b, 8b and 9b would be reduced to less than significant.

LAND USE
This section describes the affected environment and environmental consequences relating to land use for the LSJR project as well as the significance of the impacts and mitigation measures to reduce impacts.

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ENVIRONMENTAL SETTING
Regulatory Framework
Laws, regulations and requirements that apply to land use are listed below and summarized in Chapter 7.

Federal
 Executive Order 11988, Floodplain Management
 Farmland Protection Policy Act (FPPA)
 Federal Relocation Act
State
 California Land Conservation Act of 1965 (Williamson Act) Local
 San Joaquin County Multi-Species Habitat Conservation and Open Space Plan (SJMSCP) (SJCOG 2000)
 City of Lathrop General Plan (2004)
 City of Stockton General Plan (2007)
 San Joaquin County General Plan (2007)
• City of Manteca General Plan 2023 (2013)
Existing Conditions
The headwaters of San Joaquin watershed are mountainous and in open space usage. Downstream, land use within the floodplain is characterized by scattered rural-residential development and isolated centers of urban development surrounded by extensive agricultural development.

Stockton and RD 17
The city of Stockton has commercial, government, industrial and residential areas. It is the fourth most populous city in California’s Central Valley. Residential uses are concentrated in the north, above the Lower Calaveras River and civic, business and industrial uses are concentrated to the south. The area south of the Lower Calaveras River is considered downtown Stockton and consists of commercial and government uses.

The Stockton Deep Water Ship Channel, located in the southern portion of the city, plays an important role in the import and export of agricultural supplies and commodities.

Stockton has established three increasingly inclusive areas that define the extent of planning efforts relative to anticipated development over time (Figure 5-16). The city boundary defines the area of lands that are already annexed. The sphere of influence (SOI) defines the city’s physical limits and service areas. The proposed SOI defines the area expected to be annexed and developed for urban land use by 2035. The Stockton General Plan anticipates and plans for a mixture of urban development, including commercial, industrial, residential and other uses.

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San Joaquin County, CA Affected Environment and Environmental Consequences The Weston Ranch development is an existing residential development located in the northern portion of RD 17. The Weston Ranch development is primarily low density residential with scattered services and schools. In the southern portion of RD 17, land uses are primarily pasture, row crops and orchards.

According to the Stockton General Plan (2007), the area just south of Weston Ranch is planned for development including villages, commercial, administration professional and industrial uses. Villages include many different categories of housing and services with mixed densities.

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San Joaquin County, CA Affected Environment and Environmental Consequences Figure 5-16: Stockton Planning Boundaries
Source: City of Stockton 2007a.

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San Joaquin County, CA Affected Environment and Environmental Consequences Agriculture
The California Land Conservation Act of 1965, commonly referred to as the Williamson Act, enables local governments to enter into contracts with private landowners for the purpose of restricting specific parcels of land to agricultural or related open space use. In return, landowners receive property tax assessments, which are much lower than normal because they are based upon farming and open space uses as opposed to full market value. Local governments receive an annual subvention of forgone property tax revenues from the State via the Open Space Subvention Act of 1971. In 1998, the California Legislature enhanced the Williamson Act with the Farmland Security Zone (FSZ) provisions. These provisions offer landowners greater property tax reduction in return for a minimum rolling contract term of 20 years (CDC, 2010:1) In 2009, San Joaquin County had 60,059 acres (11.24 percent) of its contracts in FSZ’s. State financial support for the Williamson Act was recently eliminated; however, Senate Bill 863 was passed in 2010 as a short term solution for preserving the program. As of January 1, 2011, counties are allowed to establish new contracts with a reduction in terms from 10 to 9 years and a reduction of tax benefits by 10 percent. In 2008, 6,600 acres equaling almost 70 percent of the agricultural parcels in San Joaquin County, were covered by Williamson Act Contracts (Figure 5-17). Of these, 552 parcels were within the Stockton SOI. 5.8 percent of all enrolled acres in the county were subject to notices of nonrenewal in 2006 (San Joaquin County, 2009). Nonrenewals are often filed with the anticipation of converting farmland to other uses (CDC, 2010:7). Since 2008, San Joaquin County has shown a decrease in contract renewals.

The San Joaquin County General Plan (2007) designates 83.2 percent of lands outside of the accepted Spheres Of Influence for Lodi, Stockton, Lathrop and Manteca as agricultural and outlines a number of policies concerning its governance of land use within the county. It is the county’s policy, among others, to: (1) restrict the use of lands designated as agricultural to uses that are compatible with agricultural practices, including natural resource management, open space, outdoor recreation and enjoyment of scenic beauty; (2) protect the riparian habitat along the rivers and natural waterways to the extent possible; (3) deny all uses that intrude into or are located adjacent to an agricultural area if they are detrimental to continued agricultural usage of the surrounding area; (4) promote and protect agriculture as the primary industry of the county; (5) minimize conflict between various land uses resulting from urban expansion; and, (6) promote the diversification and growth of the local economy.

Stockton adopted a right-to-farm ordinance (Municipal Code Section 16.36.040) that recognizes that agricultural operations frequently become the subjects of nuisance complaints and seeks to reduce the premature conversion of farmland by clarifying the circumstances under which an agricultural operation may be considered a nuisance. The ordinance declares it the policy of Stockton that commercial agricultural uses in the SOI or areas not annexed by Stockton, are a priority use and inconveniences or discomforts arising from such shall not be a nuisance. The ordinance also requires discretionary development approvals to require a good faith effort to coordinate with adjacent agricultural operations to reduce potential conflicts.

There are no NRCS conservation easements on lands in the study area.

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San Joaquin County, CA Affected Environment and Environmental Consequences Figure 5-17: Williamson Act Contracts in the Study Area ATTACHMENT D 1337
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The Stockton General Plan is a land use and development plan that is required by state law. These regulations are designed to allow Stockton to manage growth while providing expanded employment opportunities, creating a mix of housing and supporting uses and ensuring that impacts to natural and cultural resources are avoided or minimized. While city policies support continued agricultural uses, provide funding for agricultural and open space programs, reduce conflicts between agricultural and urban uses and coordinate regional efforts to preserve farmland within San Joaquin County, the Stockton General Plan proposes land use changes to existing zoning that would result in substantial conversion of farmland to non-agricultural uses.

The San Joaquin Local Agency Formation Commission (LAFCO) cannot approve Stockton’s proposed changes to its SOI if the area includes lands under a Williamson Act contract. Section 56426.5 of the California Code of Regulations allows LAFCO to approve a change to the SOI when the area includes land under a Williamson Act contract if certain findings can be made. One of the findings that can be made is that “the change would facilitate planned orderly and efficient patterns of land use or provision of services and the public interest in the change substantially outweighs the public interest in the current continuation of the contract beyond its current expiration date.” Because the Stockton General Plan provides for the planned orderly and efficient use of land, requiring the development of master plans prior to the development of most of the non-urbanized land within the proposed SOI, LAFCO could make the finding necessary to approve the proposed expanded SOI. The current SOI for the City of Stockton was approved by LAFCO in September 2008.

The policies and actions of Stockton’s General Plan would result in the conversion of up to 17,230 acres of Prime Farmland, 1,260 acres of Unique Farmland and 3,190 acres of Farmland of Local Importance to nonagricultural uses and constitute a significant impact on these valuable resources (City of Stockton, 2007).

The majority of farmlands within Stockton’s SOI are not located within the FEMA 100-year floodplain and development of these lands is not limited by lack of available flood insurance. Once contracts expire, these lands are likely to be developed for commercial or residential use to compensate for the substantial increase in property taxes. San Joaquin County has designated most of the undeveloped lands within the proposed Stockton SOI as agricultural lands. However, these lands could be zoned for development once annexed by Stockton.

New development within the Stockton SOI would minimize potential incompatibilities between agricultural and urban uses through the careful allocation of land uses, the layout of roads, parks and public facilities, density controls and transfers, design guidelines for buildings and public and private improvements and possibly the use of buffers that restrict uses adjacent to agricultural land. Agriculture is a significant socioeconomic driver in the study area and surrounding region and it is important to Stockton residents that new development minimizes loss of agricultural land. The Stockton General Plan contains a number of policies that provide for the long term preservation and orderly conversion of farmland within Stockton’s SOI and planning area. There are currently no development or flood risk reduction projects planned for the areas outside the proposed SOI.

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ASSESSMENT METHODS AND BASIS OF SIGNIFICANCE
Assessment Methods
This assessment is based upon a literature and accepted standards of professional practice.

Basis of Significances
A project alternative would create a significant land use impact if it would:
 Conflict with any applicable land use plan, policy or regulation of an agency with jurisdiction over the project and adopted for the purpose of avoiding or mitigating an environmental effect;  Conflict with any applicable habitat conservation plan or natural community conservation plan; or  Result in unnecessary and unavoidable conversion of substantial areas of Prime Farmland, Unique Farmland or Farmland of Local Importance to nonagricultural use.

Effects and Mitigation Measures
ALTERNATIVE 1 - NO ACTION
Under the No Action Alternative, USACE would not construct the project and the city of Stockton and surrounding areas would continue to be at risk of flooding. A catastrophic flood event could result in damage to homes, City and County government facilities and many other properties. The Stockton General Plan would be implemented and development within RD 17 would occur as planned. While the RD 17 area is currently FEMA certified, this area would still be protected by levees and would remain at risk of flooding. If a levee failure or flood event were to occur, this urban area could be at risk of additional floodrelated damages.

Stockton would continue to enforce its Right-to-Farm Ordinance (Municipal Code Section 16.36.040), that protects owners of agricultural land at the urban fringe from unwarranted nuisance suits brought by surrounding landowners and provides for resolution of urban-agricultural disputes. An Agricultural Mitigation Fee would be implemented as a private, market-based approach to mitigate the loss of agricultural land. The mitigation fee would be used to acquire easement or fee interest in agricultural land that restricts the use to agricultural production in perpetuity. These measures would reduce and partially offset farmland conversion impacts. Nonetheless, even with the mitigation fee, design provisions, agricultural buffer and Right-to-Farm Ordinance included in the proposed General Plan, a substantial area of Prime Farmland would be converted to urban uses.

The proposed urban land use designations contained in the city limits and proposed SOI would in time lead to the conversion of farmland to urban uses as the Stockton General Plan is implemented. The Stockton General Plan designates agricultural land within the SOI and on Urban Reserve lands outside the SOI as supporting urban uses in the future. As a result of these urban designations, owners of farmland under Williamson Act contracts may be encouraged to file for non-renewal or early cancellation of their contracts in anticipation of developing their properties.

The No Action Alternative could result in scouring of agricultural land and the long-term loss of topsoil in areas within several hundred feet of the levee breach, which could result in long-term loss of Important Farmland in those areas. Flooding resulting in the destruction of agricultural land would have little to no impact related to the cancellation of Williamson Act contracts. However, in the event of simultaneous levee failures in more than 1 location, adverse effects would be more widespread. Flooding of agricultural areas would likely destroy or damage agricultural outbuildings and residences, leading to reduction in agricultural ATTACHMENT D 1339
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Lands outside of Stockton’s city limits are under the jurisdiction of San Joaquin County, which designates these lands as agricultural. Any growth beyond existing development would result in impacts on Prime Farmland; however, Stockton and San Joaquin County implement numerous measures to limit the effects of growth on farmland conversion and on the daily operation of farmland. If a flood event occurs, Prime Farmland could be affected as the flood debris, sediment and waste could result in the land being less productive for farming. It could take many years to clear the lands and return them to production.

The magnitude of the impact of flooding resulting from levee failure would depend on the location of the levee breach, severity of the storm and river flows at the time of flooding. Predicting these events and providing a determination of significance is not possible based on the information available at this time.

Therefore identification of potential effects is too speculative for meaningful consideration.

ALTERNATIVE 7A
It is anticipated that several staging areas, stockpile areas and temporary access haul roads would be developed on agricultural, vacant or undeveloped lands in during project construction. The majority of these lands would be returned to their original use following the completion of construction. Alternative 7a would include the conversion of 1 acre of farmland along the Calaveras River. The removal of 1 acre of farmland within the study area would be less than significant because of the abundance of farmland that would remain in the study area. Additionally, the removal of 1 acres of farmland to construct the project would be significantly less than the effects that could occur during a flood event. This land represents only a small fraction of the total agricultural lands within San Joaquin County.

Some residential and commercial properties adjacent to existing levees would be permanently converted to flood easements or FRM structures. Several of the levee improvements proposed would require land acquisition and may require removal of residences to accommodate the expanded footprint of the levee system. Permanent land acquisition may be necessary for implementation of adjacent levee improvements, relief wells, seepage and stability berms and setback levees. This would occur in most areas of construction along the entire project. Where residential and commercial property back up to construction areas, a swath of land at the back of the properties could be converted to FRM structures. This is primarily the case when properties are extremely close to the existing levee and sometimes within the levee footprint. In many cases, this includes the back yards, pools, out-buildings and landscapes of residents. Based on preliminary design and the maximum footprint, land conversion of residential and commercial property would occur along the entire length of Mosher Slough south levee, Shima Tract, Tenmile Slough, Lower Calaveras River, French Camp Slough and a small area along the SJR.

In addition, sufficient land will need to be acquired to establish an appropriate maintenance corridor at the landside toes of all improved levees. Specific project requirements for right-of-way to construct the project would be determined at the final design phase prior to construction. Permanent acquisition, relocation and compensation services would be conducted in compliance with Federal and State relocation laws, which are the Uniform Act of 1970 (42 USC 4601 et seq.) and implementing regulation, 49 CFR Part 24; and California Government Code Section 7267 et seq. These laws require that appropriate compensation be provided to displaced landowners and tenants and that residents be relocated to comparable replacement housing.

Much of the study area was remapped by FEMA in October 2009, with floodplain designations of X (Levee), A, AE, AH and AO. Because the majority of the study area is currently designated Zone X, there are no development restrictions from a Federal perspective. The communities face potential development restrictions under California Senate Bill 5, which requires provision of 200-year (1/200 ACE) protection ATTACHMENT D 1340
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San Joaquin County, CA Affected Environment and Environmental Consequences for urban and urbanizing areas with population greater than 10,000. However, the majority of the Alternative 7a study area is built out and not likely to see any increase in floodplain development as a result of the proposed levee improvements.

The changes in land use from the implementation of Alternative 7a do not conflict with land use plans, policies or regulations and would not conflict with master plans, policies or regulations because, overall, affecting the 156 acres of land is small compared to the city and county. Effects for the majority of these acres would be less than significant because the project would comply with associated land acquisition and relocation regulations. However, because Alternative 7a would result in direct and indirect effects resulting in the permanent loss of SRA, the project would conflict with the San Joaquin County MultiSpecies Habitat Conservation and Open Space Plan, resulting in significant and unavoidable impacts. The socioeconomic effects of displacement of residents and commercial facilities are in Section 5.13.

ALTERNATIVE 7B
Impacts to land use for Alternative 7b include all impacts discussed for Alternative 7a, with the addition of any land use impacts associated with the proposed levee improvements in RD 17. Within RD 17, there are 12,800 acres that are still in agricultural production, of which 5,300 acres are slated for urban development by the Stockton, Manteca and Lathrop General Plans. These plans are currently under revision and it is likely that the acreage may be reduced. Improving the levees in RD 17 to meet the State’s Urban Levee Design Criteria would remove constraints to future development in this area. This would be a significant effect on land use for Alternative 7b and no mitigation would be possible if this alternative were to be implemented.

This alternative would result in the permanent conversion of 30 acres of farmland to flood control easements in several areas of the project. Along the SJR south of the Weston Ranch development, there are a variety of crops orchards and associated irrigation channels that would be impacted by the project. The construction footprint runs along the perimeter of land currently being farmed and would reduce the area of production, but would not divide the farm. The San Joaquin Tie Back Levee would require the acquisition of a 130-foot wide and 2-mile long stretch of land separating some farms into small fragments. Because the project area is abundant with farmland, this would represent 0.2 percent of the overall existing farmland in the area or

0.4 percent of the farmland currently not proposed for redevelopment. Due to the low percentage of farmland affected by the proposed alternative, the effects are considered less than significant with the implementation of mitigation. Permanent acquisition, relocation and compensation services would be conducted in compliance with Federal and State relocation laws, which are the Uniform Act of 1970 (42 USC 4601 et seq.) and implementing regulation, 49 CFR Part 24; and California Government Code Section 7267 et seq. These laws require that appropriate compensation be provided to displaced landowners and tenants and that residents be relocated to comparable replacement housing.

The changes in land use from the implementation of Alternative 7b do not conflict with land use plans, policies or regulations. Land use changes do not conflict with master plans, policies or regulations, because overall the 366 acres of land being converted is small compared to the city and county. Effects for the majority of these acres would be less than significant because Alternative 7b would comply with associated land acquisition and relocation regulations. However, because Alternative 7b would result in direct and indirect effects from the permanent loss of SRA habitat, Alternative 7b would conflict with the San Joaquin County Multi-Species Habitat Conservation and Open Space Plan, resulting in significant and unavoidable impacts. The socioeconomic effects of displacement of residents and commercial facilities are in Section 5.13.

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San Joaquin County, CA Affected Environment and Environmental Consequences ALTERNATIVE 8A
Impacts to land use for Alternative 8a would include all impacts discussed for Alternative 7a, with the addition of any land use impacts associated with the additional levee improvements proposed under this alternative on the Calaveras River and Stockton Diverting Canal. Based on preliminary design and the maximum footprint, land conversion of residential and commercial property would be greater than described in Alternative 7a and much less than those described in 7b because no construction would occur in RD 17.

Alternative 8a would include the conversion of 2 acres of farmland along the Calaveras River. There are some large orchards that would have a small area (about one to two rows of trees) removed to construct the project in this reach. The removal of 2 acres of farmland within the study area would be less than significant, because of the abundance of farmland that would remain. Additionally, the removal of 2 acres of farmland to construct the project would be significantly less than the effects that could occur during a flood event.

Similar to Alternative 7a, there could be land acquisition under Alternative 8a along the Stockton Diverting Canal and Calaveras River that may require removal of residences or commercial facilities to accommodate the expanded footprint of the levee system. Permanent land acquisition may be necessary for implementation of adjacent levee improvements. In addition, sufficient land will need to be acquired to establish an appropriate maintenance corridor at the landside toes of all improved levees. Permanent acquisition, relocation and compensation services would be conducted in compliance with Federal and State relocation laws, which are the Uniform Act of 1970 (42 USC 4601 et seq.) and implementing regulation, 49 CFR Part 24; and California Government Code Section 7267 et seq. These laws require that appropriate compensation be provided to displaced landowners and tenants and that residents be relocated to comparable replacement housing.

The changes in land use from the implementation of Alternative 8a do not conflict with land use plans, policies or regulations. Land use changes would not conflict with master plans, policies or regulations because overall the 219 acres of land being impacted is small compared to the city and county. Effects for the majority of these acres would be less than significant because the project would comply with associated land acquisition and relocation regulations. However, because Alternative 8a would result in direct and indirect effects from the permanent loss of SRA, the project would conflict with the San Joaquin County Multi-Species Habitat Conservation and Open Space Plan, resulting in significant and unavoidable impacts. The socioeconomic effects of displacement of residents and commercial facilities are in Section

5.13. ALTERNATIVE 8B
Impacts to land use for Alternative 8b include all impacts discussed above for Alternative 7b, with the addition of the additional land use impacts associated with the levee improvements proposed on the Calaveras River and Stockton Diverting Canal.

Alternative 8b would include the conversion of 2 acres of farmland along the Calaveras River. There are some large orchards that would have a small area (about one to two rows of trees) removed to construct the project in this reach. The removal of 2 acres of farmland within the study area would be less than significant because of the abundance of farmland that would remain. The removal of 2 acres of farmland to construct the project would be significantly less than the effects that could occur during a flood event.

Similar to Alternative 8a, there could be land acquisition under Alternative 8b along the Stockton Diverting Canal and Calaveras River that may require removal of residences or commercial facilities to accommodate the expanded footprint of the levee system. Permanent land acquisition may be necessary for ATTACHMENT D 1342
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San Joaquin County, CA Affected Environment and Environmental Consequences implementation of adjacent levee improvements. In addition, sufficient land will need to be acquired to establish an appropriate maintenance corridor at the landside toes of all improved levees. Permanent acquisition, relocation and compensation services would be conducted in compliance with Federal and State relocation laws, which are the Uniform Act of 1970 (42 USC 4601 et seq.) and implementing regulation, 49 CFR Part 24; and California Government Code Section 7267 et seq. These laws require that appropriate compensation be provided to displaced landowners and tenants and that residents be relocated to comparable replacement housing.

The changes in land use from the implementation of Alternative 8b do not conflict with land use plans, policies or regulations. Land use changes would not conflict with master plans, policies or regulations because overall the 428 acres of land being impacted is small compared to the city and county. Effects for the majority of these acres would be less than significant because the project would comply with associated land acquisition and relocation regulations. However, because Alternative 8b would result in direct and indirect effects from the permanent loss of SRA, the project would conflict with the San Joaquin County Multi-Species Habitat Conservation and Open Space Plan, resulting in significant and unavoidable impacts. The socioeconomic effects of displacement of residents and commercial facilities are in Section

5.13. ALTERNATIVE 9A
Impacts to land use for Alternative 9a would include all impacts discussed for Alternative 7a, with the addition of any land use impacts associated with the Mormon Channel flood bypass. The Old Mormon Slough area is currently a dry channel with scattered trees that would be restored to allow a flow of 1,200 cfs during flood events. This flow would not require the construction of levees. Road crossing along Old Mormon Slough are in Section 5.15. Approximately 1 acre of farmland would be converted to permanent flood control use for the construction of the Mormon Channel control structure.

The land in Old Mormon Slough is zoned primarily as general industrial lands, with some parcels zoned for the Port’s usage. Most of the land along Old Mormon Slough is vacant, with the exception of a few road crossings. This area attracts public dumping and waste disposal as there is no restricted access. The restoration of the channel would improve the current conditions and could restore some habitat that has deteriorated over the years since the Stockton Diversion Channel was constructed. This would be a beneficial impact on land use, since illegal dumping could decrease and habitat could establish.

The changes in land use from the implementation of Alternative 9a do not conflict with land use plans, policies or regulations. Land use changes would not conflict with master plans, policies or regulations because overall the 189 acres of land being impacted is small compared to the city and county and effects for the majority of these acres would be less than significant because the project would comply with associated land acquisition and relocation regulations. However, because the Alternative 9a would result in direct and indirect effects from the permanent loss of SRA, the project would conflict with the San Joaquin County Multi-Species Habitat Conservation and Open Space Plan, resulting in significant and unavoidable impacts. The socioeconomic effects of displacement of residents and commercial facilities are in Section 5.13.

ALTERNATIVE 9B
Impacts to land use for Alternative 9b include all impacts discussed above for Alternative 7b, with the addition of the land use impacts associated with the Old Mormon Channel flood bypass. Approximately 31 acres of farmland would be converted to flood control uses under this alternative, including 30 acres as detailed under Alternative 7b and an additional 1 acre associated with the construction of the Old Mormon Channel control structure. Because the project area is abundant with farmland, this would represent 0.2 ATTACHMENT D 1343
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San Joaquin County, CA Affected Environment and Environmental Consequences percent of the overall existing farmland in the area or 0.4 percent of the farmland currently not proposed for redevelopment. Due to the low percentage of farmland affected by the proposed alternative, the effects are considered less than significant with the implementation of mitigation. Permanent acquisition, relocation and compensation services would be conducted in compliance with Federal and State relocation laws, which are the Uniform Act of 1970 (42 USC 4601 et seq.) and implementing regulation, 49 CFR Part 24; and California Government Code Section 7267 et seq. These laws require that appropriate compensation be provided to displaced landowners and tenants and that residents be relocated to comparable replacement housing.

The changes in land use from the implementation of Alternative 9b do not conflict with land use plans, policies or regulations. Land use changes would not conflict with master plans, policies or regulations because overall the 401 acres of land being impacted is small compared to the city and county and effects for the majority of these acres would be less than significant, because the project would comply with associated land acquisition and relocation regulations. However, because Alternative 9b would result in direct and indirect effects from the permanent loss of SRA, the project would conflict with the San Joaquin County Multi-Species Habitat Conservation and Open Space Plan, resulting in significant and unavoidable impacts. The socioeconomic effects of displacement of residents and commercial facilities are in Section 5.13.

MITIGATION
Property acquisition would be consistent will all applicable laws and regulations. If relocation of people, homes or businesses would be minimized to the extent feasible and consistent with the project purpose and compensated under the Federal Relocation Act. In addition, implementation of compensatory habitat mitigation would off-set impacts on sensitive species, other fish and wildlife and their habitats. This would this would be consistent with the overall purpose of the Multispecies Habitat Conservation and Open Space Plan. While these mitigation measures would reduce impacts, they would remain significant and unavoidable because of direct and indirect effects of the permanent loss of SRA and conflict with the Multispecies Habitat Conservation and Open Space Plan.

TRANSPORTATION
This section describes the affected environment and environmental consequences related to transportation for the LSJR project and the significance of the impacts and mitigation measures to reduce impacts.

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ENVIRONMENTAL SETTING
Regulatory Framework
Laws, regulations and requirements that apply to transportation are listed below and summarized in Chapter

7. Federal
 Title 23 of the Code of Federal Regulations (CFR)
 Title 23 of the U.S. Code (USC)
State
 California Streets and Highways Code
Local
 Congestion Management Program (CMP) (CA Government Code, Section 65089)  City of Lathrop General Plan (2004)
 City of Stockton General Plan (2007)
 San Joaquin County General Plan (2007)
 City of Manteca General Plan 2023 (2013)
 2014 Regional Transportation Plan and Sustainable Communities Strategy, (adopted by SJCOG June 26, 2014)
Existing Conditions
Flow of traffic and safety conditions are typically categorized according to Level of Service (LOS) on a scale from A to F. A roadway categorized as LOS A supports free-flow operations where traffic flows at or above posted speed limits and all motorists have complete mobility between lanes. A roadway categorized as LOS F represents a breakdown in vehicular flow where every vehicle moves in response to the vehicle in front of it and frequent slowing and stopping are required. A roadway functioning at LOS C represents conditions with free-flow operations and few restrictions. Planners typically establish a threshold of LOS C to provide the most efficient flow of traffic without affecting driver comfort and safety. The roadways below are those within the project area which cross the SJR and tributaries via either low water crossing or bridges and may be impacted by the project (Figure 5-18).

SJCOG is the Congestion Management Agency for San Joaquin County. It adopted its first Congestion Management Program (CMP) in November 1991. SJCOG implements the Congestion Management Program and the Federal Congestion Management Process. The update to the current CMP was adopted by the SJCOG Board of Directors in October 2012 (SJCOG, 2014:2-3).

State-Maintained Highways
One Interstate Highway, I-5 and four state highways, Highway 99, Highway 4, Highway 26 and Highway 88, cross San Joaquin County near the study area. All of these roads are regionally significant and are included in the Congestion Management Program for San Joaquin County.

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I-5 and Highway 99
I-5 traverses Washington, Oregon and California from north to south, connecting Vancouver, Canada to Tijuana, Mexico and is an important corridor for both commuter and freight traffic. As I-5 enters the Central Valley from the south, Highway 99 splits from it and travels through the Central Valley East of the SJR and services the larger population centers of the valley, including Bakersfield and Fresno. I-5 skirts the more remote western extremity of the valley and crosses the Calaveras River and Old Mormon Slough in Stockton and the SJR in RD 17. Highway 99 crosses the Stockton Diverting Canal and Mormon Channel.

In Central Stockton at the interchange with Highway 4, I-5 has an Annual Average Daily Traffic (AADT) of 139,000. In RD 17 at Lathrop Road, I-5 has an AADT of 98,000. In Central Stockton at Hammer Lane, Highway 99 has an AADT of 64,000. In RD 17 at the junction of Highway 120, Highway 99 has an AADT of 66,000 (Caltrans, 2012).

Highway 4
Highway 4 runs east-west and connects I-5 to Highway 99 north of the Old Mormon Slough. The existing LOS varies from C to D, according to the Stockton General Plan (City of Stockton, 2007a), with an AADT of 15,400 to 96,000 (Caltrans, 2012).

State Route 88/Waterloo Road
Waterloo Road is a four lane road which runs generally northeast and is locally and Federally-classified as a minor arterial road. It originates at Wilson Way and crosses the Stockton Diverting Canal before it becomes State Route 88. The AADT for Highway 88 at its junction with Highway 99 is 24,100 (Caltrans, 2012).

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San Joaquin County, CA Affected Environment and Environmental Consequences State Route 26/Fremont St.

Fremont Street is a four lane road which connects I-5 to Highway 99. As it exits Stockton, Fremont Street becomes Highway 26 and crosses the Stockton Diverting Canal. Highway 26 roughly parallels Highway 88 as it extends onward through agricultural areas and communities to the northeast. The AADT for Highway 26 at its junction with Highway 99 is 15,500 (Caltrans, 2012).

State Route 120
This road generally runs east and west, connecting the valley with the Sierra Nevada Mountains. State Route 120 originates as a freeway that intersects I-5 and extends I-205 through Manteca. In east Manteca, this freeway ends at SR 99 and becomes a highway that continues east through agricultural lands, the foothills of the Sierra Nevada and Yosemite National Park, ending at U.S. Route 6 in Mono County.

City- and County-Managed Roadways
The different types of roadways in the project area include arterials, collectors and local roads. Arterials provide access to shopping, employment and recreation and comprise the main network for traffic within and between communities. Collectors are the main interior streets carrying traffic from neighborhoods and business areas to higher level roads. Local facilities are two lane streets providing local access and service in agricultural and rural areas of the county. Roads which cross the SJR and tributaries in the LSJRFS study area are briefly described.
 6 vehicle bridges, which are two-lane minor arterial roadways, cross the Stockton Diverting Canal:

Cherokee Road, Main Street, Highway 26, Wilson Way, Highway 88, Highway 99.  6 vehicle bridges cross the Calaveras River: West Lane (4-lane, minor arterial), El Dorado Street, Pacific Avenue, Pershing Avenue and I-5. Between Pacific Avenue and Pershing Avenue, a footbridge provides pedestrian access across the river into University of the Pacific. A second footbridge is located east of West Lane just west of the Union Pacific Railroad’s Fresno subdivision.
 Five vehicle bridges cross Mosher Slough: Mariners Drive, Interstate 5, Kelley Drive, Don Avenue and Thornton Road. A footbridge provided pedestrian access across the slough between Yarmouth Drive and Bainbridge Place.
 4 vehicle bridges cross the SJR: Howard Road (minor arterial), Charter Way, Highway 4 and I-5.  One pedestrian bridge and 22 vehicle bridges and low-water crossings cross Old Mormon Slough, including vehicle bridges for Interstate 5 and Highway 4.  A 2-lane vehicle bridge crosses Fourteenmile Slough at Feather River Drive.  2 vehicle bridges cross French Camp Slough: Carolyn Weston and Manthey Road.

Haul routes have not yet been designated but would be analyzed in subsequent CEQA and NEPA environmental documentation. The project area would be accessed from I-5, Highway 99 and major arterial roadways, which would connect to minor arterial, local and connector roadways to access study areas.

Access to levees would be provided from residential streets and rural agricultural roads which connect to maintenance ramps. In addition, public access to the levee and river would be provided at Buckley Cove Boat Launch, on the SJR north of the Calaveras, Louis Park Boat Launch at the confluence of Smith Canal and Dos Reis Regional Park on the SJR north of Old River.

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San Joaquin Regional Transit District provides fixed route service throughout the Stockton Metropolitan Area and provides subscription commuter services connecting Stockton with Livermore, Dublin, Mountain View, Palo Alto, Pleasanton, Santa Clara, Sunnyvale, San Jose and Sacramento.

Railroad
Stockton is served by two national rail lines (the Union Pacific Railroad [UPRR] and the Burlington Northern Santa Fe Railroad [BNSF]) and two short line railroads (Central California Traction Company [CCT] and Stockton Terminal and Eastern Railroad [STE]). UPRR owns 2,773 track miles in California.

BNSF owns 1,155 track miles and operates more than 2,000 track miles in California. STE operates freight service in Stockton along 25 miles of leased UPRR rail lines (UPRR, 2013) and CCT operates freight service along 16 miles of track between Stockton and Lodi (UPRR, 2013). Commodities carried include agriculture, asphalt, cement, food processing, lumber, steel and chemical transportation.

The Altamont Commuter Express provides passenger service between Stockton and San Jose. Service currently consists of four westbound morning trains and four eastbound evening trains. Amtrak also makes stops in Stockton and provides passenger service to the rest of the nation.

ASSESSMENT METHODS AND BASIS OF SIGNIFICANCE
Assessment Methods
This assessment is based upon a literature review and accepted standards of professional practice.

Basis of Significance
A project alternative would have a significant impact on traffic or transportation if it would:
 Cause an increase in traffic, which is substantial in relation to the existing traffic load and capacity of the street system;
 Conflict with an applicable congestion management plans (CMP), including, but not limited to, LOS standards and travel demand measures or other standards established by the county congestion management agency for designated roads or highways;
 Result in a change in air traffic patterns, including either an increase in traffic levels or a change in location that results in substantial safety risks;
 Substantially increase hazards due to a design feature (such as sharp curves or dangerous intersections) or incompatible uses (such as farm equipment);  Result in inadequate emergency access;
 Result in inadequate parking capacity; or
 Conflict with adopted policies, plans or programs supporting public transit, bicycle or pedestrian facilities or otherwise decrease the performance or safety of such facilities.

To account for the large percentage of heavy trucks associated with typical construction projects, the Institute of Transportation Engineers recommends a threshold level of 50 or more new peak-direction trips during the peak hours. Therefore, an alternative would cause an increase in traffic that is substantial in relation to the existing traffic load and capacity and result in a significant impact related to traffic, if it would result in 50 or more new truck trips during the morning or evening peak hours.

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San Joaquin County, CA Affected Environment and Environmental Consequences Effects and Mitigation Measures
None of the project alternatives would involve local transportation land use changes as a result of flood management improvements. Project construction under all alternatives would not increase air traffic levels or introduce new safety risks related to aviation. Therefore, hazards related to design features, parking capacity, land use or air traffic are not discussed in further detail.

The Stockton General Plan denotes several proposed and existing bicycle routes within the project area.

These bicycle paths would either cross over the proposed levee improvements or could be built on the levees. Levee improvement would not preclude development of these alternative transportation routes and there would be no impact. Therefore, alternative transportation routes are not discussed in further detail.

ALTERNATIVE 1 - NO ACTION
Under the No Action Alternative, construction of the project would not occur. However, if a flood occurs, there would be a substantial increase in traffic due to debris removal and clean-up. Additionally, roads could be covered with sediment and debris, making emergency access difficult. Bridges and railroads could also be damaged during a flood event, making access to areas impossible. This would be a significant and unavoidable impact on transportation because of the increase in traffic during clean-up and the inadequate emergency access during and immediately following a flood event.

ALTERNATIVE 7A
The SJCOG CMP is the applicable CMP for Alternative 7a. The CMP emphasizes travel demand measures to reduce the number of miles driven per capita; infrastructure improvements to reduce SOV trips; land use regulations to encourage the use of alternative modes of transportation instead of cars; and monitoring and enforcement of travel demand measure implementation by development projects. Homes, businesses and other traffic generating development will not be constructed under Alternative 7a. Because construction related traffic is not targeted in the CMP to reduce congestion, no conflict with the CMP would occur with implementation of Alternative 7a.

Alternative 7a would result in minimal, short term impacts on traffic but would not substantially restrict emergency access. Because homes, businesses and other traffic-generating development would not be constructed under Alternative 7a and because construction related traffic is not targeted in the CMP, Alternative 7a would not conflict with the SJCOG CMP.

The construction impacts would be the smallest of all action alternatives. Flood risk would be reduced to existing urban development. During the peak of construction, a maximum of 327 haul trips per day would be required to transport the construction materials to the site and a maximum crew of 60 workers would commute to the site each day during peak hours. Traffic would increase on local roadways associated with construction trips. In addition, temporary lane closures associated with levee improvements and with construction staging and laydown areas could cause or contribute to temporary increases in traffic levels as traffic slows down on local, collector and arterial streets. Increased traffic congestion on road segments and intersections would temporarily interfere with the use of main roadways for emergency evacuation routes.

After construction of Alternative 7a is complete, however, the risk of inundation to freeway onramps and off-ramps would be reduced, which would improve access for emergency responders and reduce delays of local and regional residents returning to residences after floods.

For some sites, truck trips may involve hauling materials through residential areas that are not designated truck routes. Additionally, haul routes may occur in the vicinity of schools throughout the project area.

When possible, construction schedules would avoid routes that impact schools during the school year.

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San Joaquin County, CA Affected Environment and Environmental Consequences However, the project would impact routes to schools even with mitigation and impacts to schools would be significant and unavoidable.

The proposed levee repairs under Alternative 7a would cross 2 railroad bridges. Freight and passenger service could be disrupted for a day or more if necessary to complete cutoff wall construction beneath these bridges. In some cases, levee height fixes are proposed as well, which may require modifications to the existing railway over the levee, but the extent of these modifications is not known at this time. Detailed designs of railway crossings would be completed in the design phase of the project. Effects associated with service disruption would be temporary and the railways would be reconstructed in their current alignment.

In addition, the proposed levee repairs under Alternative 7a would cross 27 roadway bridges. Construction of slurry walls could require drilling through the roadway, which would require road or lane closures and temporary disruptions of service. In some locations, there may be a levee height fix required at the roadway crossings. Levee height fixes may require modifications to the existing roadway. However, the extent of these modifications is not known at this time. Detailed designs of roadway crossings would be completed in the design phase of the project. Effects associated with service disruption would be temporary and the roadways would reconstructed in their current alignment.

Because implementation of Alternative 7a could result in temporary delays in emergency response time, temporary railroad service disruptions, hauling materials through residential neighborhoods and school zones and potential interference with evacuation routes during construction, this impact would be significant and unavoidable.

ALTERNATIVE 7B
The SJCOG CMP is the applicable CMP for Alternative 7b. Homes, businesses and other traffic generating development will not be constructed under Alternative 7b. Because construction related traffic is not targeted in the CMP to reduce congestion, no conflict with the CMP would occur with implementation of Alternative 7b. Alternative 7b would result in minimal, short-term impacts on traffic but would not substantially restrict emergency access. Because homes, businesses and other traffic-generating development would not be constructed and because construction related traffic is not targeted in the CMP, Alternative 7b would not conflict with the SJCOG CMP.

Assuming a peak crew size of 60 workers, 60 additional commuter trips would be added during peak hours.

In addition, activities would require moving large quantities of soil, construction materials and heavy equipment into and out of the study area. During the peak of construction, the number of daily round trips to haul materials would be 327. This volume is less than 10 percent of the total anticipated daily volume for any given road in the project area. Assuming a 10-hour workday, implementation of Alternative 7b would add 33 truck trips during the peak-hour period. This number is well below the significance threshold of 50 new truck trips per hour. However, roadways with a LOS of D or F may still experience a significant effect from this increase in truck traffic. It is possible that haul trucks could be distributed over several haul routes within the project area due to simultaneous construction of levee elements at different locations, reducing the number of truck trips per street.

Alternative 7b would increase traffic on local roadways associated with construction trips. In addition, temporary lane closures associated with levee improvements could cause or contribute to temporary increases in traffic levels on some local, collector and arterial streets. Increased traffic congestion on road segments and intersections could temporarily interfere with the use of main roadways for emergency evacuation routes. After construction of Alternative 7b is complete, however, the risk of inundation to freeway onramps and off-ramps would be reduced, which could improve access for emergency responders and prevent delays of local and regional residents returning to residences after floods. Construction related ATTACHMENT D 1350
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San Joaquin County, CA Affected Environment and Environmental Consequences impacts from Alternative 7b could potentially result in a significant effect on the effectiveness and performance of local circulation systems.

When possible, construction schedules would avoid routes that impact schools during the school year.

However, the project would impact routes to schools even with mitigation and impacts to schools would be significant and unavoidable.

The proposed levee repairs would cross 5 railroad bridges. Freight and passenger service could be disrupted for a day or more if necessary to complete cutoff wall construction beneath these bridges. These effects would be temporary; the alignment of the railroads would not be affected by the proposed repairs, nor would any railroads need to be permanently raised.

In addition, the proposed levee repairs under Alternative 7b would cross 35 roadway bridges and one pedestrian bridge. Construction of slurry walls could require drilling through the roadway, which would require road or lane closures and temporary disruptions of service. In some locations, there may be a levee height fix required at the roadway crossings. Levee height fixes may require modifications to the existing roadway. However, the extent of these modifications is not known at this time. Detailed designs of roadway crossings would be completed in the design phase of the project. Effects associated with service disruption would be temporary and the roadways would reconstructed in their current alignment.

Because implementation of Alternative 7b could result in temporary delays in emergency response time, temporary railroad service disruptions, hauling materials through residential areas and school zones and potential interference with evacuation routes during construction, this impact would be significant and unavoidable.

ALTERNATIVE 8A
Impacts from implementation of Alternative 8a would be similar to Alternative 7a except that it would result in additional construction on Lower Calaveras River levees and on the Stockton Diverting Canal.

Affects to transportation would be the same during peak hours as for Alternative 7a, but the duration of construction would be increased because of the larger construction footprint. During the peak of construction, each day a maximum of 327 haul trips would be required to transport the construction materials to the site and a maximum crew of 60 workers would commute to the site during peak hours. This is well below the significance threshold of 50 new truck trips per hour. However, roadways with a LOS of D or F may still experience a significant effect from this increase in truck traffic. It is possible that haul trucks could be distributed over several haul routes within the project area due to simultaneous construction of levee elements at different locations, reducing the number of truck trips per street.

Alternative 8a would increase traffic on local roadways associated with construction trips. In addition, temporary lane closures associated with levee improvements and with construction staging and laydown could cause or contribute to temporary increases in traffic levels as traffic slows down on some local, collector and arterial streets. Increased traffic congestion on road segments and intersections could temporarily interfere with the use of main roadways for emergency evacuation routes. After construction of Alternative 8a is complete, however, the risk of inundation to freeway onramps and off-ramps would be reduced, which could improve access for emergency responders and prevent delays of local and regional residents returning to residences after floods.

When possible, construction schedules would avoid routes that impact schools during the school year.

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San Joaquin County, CA Affected Environment and Environmental Consequences However, the project would impact routes to schools even with mitigation and impacts to schools would be significant and unavoidable.

The proposed levee repairs under Alternative 8a would cross 6 railroad bridges. Freight and passenger service could be disrupted for a day or more if necessary to complete cutoff wall construction beneath these bridges. In some cases, levee height fixes are proposed as well, which might require modifications to the existing railway over the levee, but the extent of these modifications is not known at this time. Detailed designs of railway crossings would be completed in PED phase. Effects associated with service disruption would be temporary and the railways would be reconstructed in their current alignment.

In addition, the proposed levee repairs under Alternative 8a would cross 39 roadway bridges. Construction of slurry walls could require drilling through the roadway, which would require road or lane closures and temporary disruptions of service. In some locations, there may be a levee height fix required at the roadway crossings. Levee height fixes may require modifications to the existing roadway. However, the extent of these modifications is not known at this time. Detailed designs of roadway crossings would be completed in the design phase of the project. Effects associated with service disruption would be temporary and the roadways would be reconstructed in their current alignment.

Because implementation of Alternative 8a could result in temporary delays in emergency response time, temporary railroad service disruptions, hauling through residential areas and school zones and potential interference with evacuation routes during construction, this impact would be significant and unavoidable.

ALTERNATIVE 8B
The SJCOG CMP is the applicable CMP for Alternative 8b. Homes, businesses and other traffic generating development will not be constructed under Alternative 8b. Because construction related traffic is not targeted in the CMP to reduce congestion, no conflict with the CMP would occur with implementation of Alternative 8b.

Alternative 8b would result in minimal, short-term impacts on traffic, but would not substantially restrict emergency access. Because homes, businesses, and other traffic-generating development would not be constructed under Alternative 8b, and because construction related traffic is not targeted in the CMP, Alternative 8b would not conflict with the SJCOG CMP. Assuming a peak crew size of 60 workers, 60 additional commuter trips would be added during peak hours. In addition, activities would require moving large quantities of soil, construction materials and heavy equipment into and out of the study area. During the peak of construction, the number of daily round trips to haul materials would be 327. This volume is less than 10 percent of the total anticipated daily volume for any given road in the project area. Assuming a 10-hour workday, implementation of Alternative 8b would add 33 truck trips during the peak-hour period.

This number is well below the significance threshold of 50 new truck trips per hour. However, roadways with a LOS of D or F may still experience a significant effect from this increase in truck traffic. It is possible that haul trucks could be distributed over several haul routes within the project area due to simultaneous construction of levee elements at different locations, reducing the number of truck trips per street.

Alternative 8b would increase traffic on local roadways associated with construction trips. In addition, temporary lane closures associated with levee improvements and with construction staging and laydown could cause or contribute to temporary increases in traffic levels as traffic slows down on some local, collector and arterial streets. Increased traffic congestion on road segments and intersections could temporarily interfere with the use of main roadways for emergency evacuation routes. After construction of Alternative 8b is complete, however, the risk of inundation to freeway onramps and off-ramps would be reduced, which could improve access for emergency responders and prevent delays of local and regional residents returning to residences after floods.

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San Joaquin County, CA Affected Environment and Environmental Consequences For some sites, truck trips may involve hauling materials through residential areas that are not designated truck routes. Additionally, haul routes may occur in the vicinity of schools throughout the project area.

When possible, construction schedules would avoid routes that impact schools during the school year.

However, the project would impact routes to schools even with mitigation and impacts to schools would be significant and unavoidable.

The proposed levee repairs under Alternative 8b would cross 8 railroad bridges. Freight and passenger service could be disrupted for a day or more if necessary to complete cutoff wall construction beneath these bridges. In some cases, levee height fixes are proposed as well, which might require modifications to the existing railway over the levee, but the extent of these modifications is not known at this time. Detailed designs of railway crossings would be completed in PED phase. Effects associated with service disruption would be temporary and the railways would reconstructed in their current alignment.

In addition, the proposed levee repairs under Alternative 8b would cross 47 roadway bridges. Construction of slurry walls could require drilling through the roadway, which would require road or lane closures and temporary disruptions of service. In some locations, there may be a levee height fix required at the roadway crossings. Levee height fixes may require modifications to the existing roadway. However, the extent of these modifications is not known at this time. Detailed designs of roadway crossings would be completed in the design phase of the project. Effects associated with service disruption would be temporary and the roadways would be reconstructed in their current alignment.

Because implementation of Alternative 8b could result in temporary delays in emergency response time, temporary railroad service disruptions, hauling through residential areas and school zones and potential interference with evacuation routes during construction, this impact would be significant and unavoidable.

ALTERNATIVE 9A
Under Alternative 9a, the project footprint and proposed activities would be the same as Alternative 7a, with the addition of a flood bypass proposed in Old Mormon Slough. In addition to the impacts described in Alternative 7a, the channel improvements proposed in Alternative 9a would require the removal of 4 channel crossings and replacement with bridges along the Old Mormon Slough alignment, including Commerce Street, Stanislaus Street, David Avenue and Gillis Road. Low water crossings for Bieghle Alley and Pilgrim Street would be incorporated into the channel area and no bridge installed. However, these are unpaved dirt access roads created by use and not part of the public road system. Detours would be required on each bridge crossing for several weeks during levee construction. Detour routes and lane closures would be minimized to the extent possible.

There are four railroad crossings on Old Mormon Slough, in addition to the two railroad bridges on the SJR affected by cutoff wall construction. In one of the Old Mormon Slough crossings, two additional culverts would be installed to supplement the four existing 8-foot culverts. Freight and passenger service could be disrupted for a day or more if necessary to complete culvert construction beneath this railroad crossing.

These effects would be temporary; the alignment of the railroads would not be affected by the proposed repairs, nor would the railroads need to be permanently raised.

Freight and passenger service could be disrupted for a day or more if necessary to complete cutoff wall construction beneath the two railroad bridges on the SJR. In some cases, levee height fixes are proposed as well, which might require modifications to the existing railway over the levee. However, the extent of these modifications is not known at this time. Detailed designs of railway crossings would be completed in the design phase of the project. Effects associated with service disruption would be temporary and the railways would be reconstructed in their current alignment.

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San Joaquin County, CA Affected Environment and Environmental Consequences In addition, the proposed levee repairs under Alternative 9a would cross 27 roadway bridges. Construction of slurry walls could require drilling through the roadway, which would require road or lane closures and temporary disruptions of service. In some locations, there may be a levee height fix required at the roadway crossings. Levee height fixes may require modifications to the existing roadway. However, the extent of these modifications is not known at this time. Detailed designs of roadway crossings would be completed in the design phase of the project. Effects associated with service disruption would be temporary and the roadways would be reconstructed in their current alignment.

Because implementation of Alternative 9a could result in temporary delays in emergency response time, temporary railroad service disruptions, hauling of materials through residential neighborhoods and school zones and potential interference with evacuation routes during construction, this impact would be significant and unavoidable.

ALTERNATIVE 9B
Under Alternative 9b, the project footprint and proposed activities would be the same as Alternative 7b, with the exception that a bypass would be constructed in Old Mormon Slough. Assuming a peak crew size of 60 workers, 60 additional commuter trips would be added during peak hours. In addition, activities would require moving large quantities of soil, construction materials and heavy equipment into and out of the study area. During the peak of construction, the number of daily round trips to haul materials would be 327.

This volume is less than 10 percent of the total anticipated daily volume for any given road in the project area. Assuming a 10-hour workday, implementation of Alternative 9b would add 33 truck trips during the peak-hour period. This number is well below the significance threshold of 50 new truck trips per hour.

However, roadways with a LOS of D or F may still experience a significant effect from this increase in truck traffic. It is possible that haul trucks could be distributed over several haul routes within the project area due to simultaneous construction of levee elements at different locations, reducing the number of truck trips per street.

Alternative 9b would increase traffic on local roadways associated with construction trips. In addition, temporary lane closures associated with levee improvements could cause or contribute to temporary increases in traffic levels on some local, collector and arterial streets. Increased traffic congestion on road segments and intersections could temporarily interfere with the use of main roadways for emergency evacuation routes. After construction of Alternative 9b is complete, however, the risk of inundation to freeway onramps and off-ramps would be reduced, which could improve access for emergency responders and prevent delays of local and regional residents returning to residences after floods. Construction related impacts from Alternative 9b could potentially result in a significant effect on the effectiveness and performance of local circulation systems.

When possible, construction schedules would avoid routes that impact schools during the school year.

However, the project would impact routes to schools even with mitigation and impacts to schools would be significant and unavoidable.

In addition to the impacts described in Alternative 7b, the channel improvements proposed in Alternative 9b would require the removal of 4 channel crossings and replacement with bridges along the Mormon Channel alignment, including Commerce Street, Stanislaus Street, David Avenue and Gillis Road. Low water crossings for Bieghle Alley and Pilgrim Street would be incorporated into the channel area and no bridge installed. However, these are unpaved dirt access roads created by use and not part of the public road system. Detours would be required on each bridge crossing for several weeks during levee construction.

Detour routes and lane closures would be minimized to the extent possible.

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San Joaquin County, CA Affected Environment and Environmental Consequences There are four railroad crossings on Old Mormon Slough, in addition to the five railroad bridges on the SJR affected by cutoff wall construction. In one of the Mormon Channel crossings, two additional culverts would be installed to supplement the four existing 8-foot culverts. Freight and passenger service could be disrupted for a day or more, if necessary, to complete culvert construction beneath this railroad crossing.

These effects would be temporary; the alignment of the railroads would not be affected by the proposed repairs, nor would the railroads need to be permanently raised.

Freight and passenger service could be disrupted for a day or more, if necessary, to complete cutoff wall construction beneath the five railroad bridges on the SJR. In some cases, levee height fixes are proposed as well, which might require modifications to the existing railway over the levee. However, the extent of these modifications is not known at this time. Detailed designs of railway crossings would be completed in the design phase of the project. Effects associated with service disruption would be temporary and the railways would be reconstructed in their current alignment.

In addition, the proposed levee repairs under Alternative 9b would cross 35 roadway bridges and 1 pedestrian bridge. Construction of slurry walls could require drilling through the roadway, which would require road or lane closures and temporary disruptions of service. In some locations, there may be a levee height fix required at the roadway crossings. Levee height fixes may require existing roadway modifications, but the extent of these modifications is not known at this time. Detailed designs of roadway crossings would be completed in PED phase. Effects associated with service disruption would be temporary and the roadways would be reconstructed in their current alignment.

Because implementation of Alternative 9b could result in temporary delays in emergency response time, temporary railroad service disruptions, hauling materials through residential areas and in school zones and potential interference with evacuation routes during construction, this impact would be significant and unavoidable.

MITIGATION
Alternative 7a and 7b mitigation proposes that during preliminary engineering and design, the project proponents (USACE, DWR and SJAFCA) shall provide notification of project construction to all appropriate railroads in the project area and shall coordinate with all railroads to minimize freight and passenger service disruptions. Notification of project construction with all appropriate railroads in the project area is to minimize freight and passenger service disruptions that would occur.

Before the start of each construction season, the primary contractors for engineering and construction shall develop a coordinated construction traffic safety and control plan to minimize the simultaneous use of roadways by different construction contractors for material hauling and equipment delivery to the extent feasible and to avoid and minimize potential traffic hazards on local roadways during construction. Items (a) through (f) of this mitigation measure shall be integrated as terms of the construction contracts. a) The plan shall outline phasing of activities and the use of multiple routes to and from off site locations to minimize the daily amount of traffic on individual roadways.

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San Joaquin County, CA Affected Environment and Environmental Consequences b) The construction contractors shall develop traffic safety and control plans for the local roadways that would be affected by construction traffic. Before the initiation of construction-related activity involving high volumes of traffic, the plan shall be submitted for review by the agency of local jurisdiction (San Joaquin County, City of Stockton or Caltrans [if applicable]) that has responsibility for roadway safety at and between project sites. The contractor would train construction personnel in appropriate safety measures as described in the plan and shall implement the plan. The plan would include the prescribed locations for staging equipment and parking trucks and vehicles. Provisions would be made for overnight parking of haul trucks to avoid causing traffic or circulation congestion. The plan shall call for the following elements:
 posting warnings about the potential presence of slow-moving vehicles;  using traffic control personnel when appropriate; and  placing and maintaining barriers and installing traffic control devices necessary for safety, as specified in Caltrans’s Manual of Traffic Controls for Construction and Maintenance Work Zones and in accordance with city/county requirements.
c) All operations would limit and expeditiously remove, as necessary, the accumulation of projectgenerated mud or dirt from adjacent public streets at least once every 24 hours if substantial volumes of soil are carried onto adjacent paved public roadways during construction. d) If needed to comply with Caltrans requirements, a transportation management plan would be prepared and submitted to Caltrans to cover any points of access from the State highway system for haul trucks and other construction equipment.
e) Before the start of the first construction season, the project proponent would enter into maintenance agreements with San Joaquin County and the City of Stockton to address maintenance and repair of affected roadways resulting from increased truck traffic. The agreements would ensure that the affected roadways are repaired to a level that is equivalent to their pre-project condition. f) Before project construction begins, the contractor would provide notification of project construction to all appropriate emergency service providers in San Joaquin County, Stockton, Lathrop and Manteca and shall coordinate with providers throughout the construction period to ensure that emergency access through construction areas is maintained.

The contractor would be required to avoid neighborhoods and school zones to the maximum extent feasible when determining haul routes. When possible, hauling in school zones would be limited to the period of summer breaks to avoid noise and traffic impacts to the schools. Any damage to residential roadways during construction would be mitigated per the requirements outlined in the traffic safety and control plan.

Alternatives 8a and 8b mitigation measures shall be implemented as described for Alternatives 7a and 7b, except that they would be expanded to include additional lands and the jurisdictions along the Stockton Diverting Canal. During preliminary engineering and design, the project proponent shall provide notification of project construction to all appropriate railroads in the project area, and shall coordinate with all railroads to minimize freight and passenger service disruptions.

Alternatives 9a and 9b mitigation measures shall be implemented as described for Alternative 7a and Alternative 7b, except that they would be expanded to include additional lands and the jurisdictions along the Old Mormon Slough. Prior to construction, USACE would coordinate with Caltrans and the City of Stockton to determine detour routes for all proposed bridge replacements. Public notification would occur prior to all bridge closures during construction.

ATTACHMENT D 1356
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San Joaquin County, CA Affected Environment and Environmental Consequences Implementation of the traffic safety and control plan (outlined in Alternatives 7a and 7b) and coordination with the railroads would reduce the transportation impacts. Because haul routes are unknown at this time, the magnitude of impacts to transportation and circulation during construction activities cannot be quantified; therefore, even with mitigation measures impacts would remain significant and unavoidable.

UTILITIES AND PUBLIC SERVICES
This section describes the affected environment and environmental consequences relating to public utilities and public services for the LSJR project and the significance of the impacts and mitigation measures to reduce impacts.

ENVIRONMENTAL SETTING
Regulatory Framework
Laws, regulations and requirements that apply to utilities and public services and use are listed below and summarized in Chapter 7.

State
 California Integrated Waste Management Act
 California Public Utilities Commission
Local
 City of Lathrop General Plan (2004)
 City of Stockton General Plan (2007)
 San Joaquin County General Plan (2007)
 City of Manteca General Plan 2023 (2013)
Existing Conditions
Water Services
San Joaquin County
Water supply in San Joaquin County is provided by surface water and groundwater. Over 50 water agencies provide services to County residents. In addition, hundreds of smaller private water systems and individual wells provide domestic and agricultural uses (San Joaquin County, 2010). The South San Joaquin County Water Supply Program addresses current and future needs of the southern part of the county, including Manteca and Lathrop. The first phase of this program became operational in 2005.

Stockton
Stockton’s potable water is provided by a combination of treated surface water from the Delta Water Supply Project and SEWD and pumped groundwater. Surface water from Calaveras River and Stanislaus River has historically provided 60 percent of the water supply in the City of Stockton Metropolitan Area. The total available surface water varies from 104,100 AF/year to 48,000 AF/year. Treatment and distribution capacity at SEWD is 56,000 AF/year (City of Stockton, 2008a).

Groundwater extraction has historically provided 40 percent of Stockton’s water supply and ranges from

0.75 to 1.0 AF/year. The long-term operational goal for sustainable groundwater yield is 0.6 AF/year (City ATTACHMENT D 1357
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San Joaquin County, CA Affected Environment and Environmental Consequences of Stockton 2007, 2008a). Groundwater quality is increasingly affected by salinity levels, pesticides and fertilizers due to continued overdraft in the basin. Although treatment options are still being evaluated, the cost of desalination may necessitate a switch from groundwater to another supply source.

The City of Stockton’s water demand as of 2004 was 68,714 AF/year. Water demand is expected to increase to 85,330 AF/year by 2015 and to 156,083 AF/year by 2035. To meet future water supply needs, the city is exploring groundwater storage projects, non-potable water supplies from local communities and raw surface water transfers from local irrigation districts. Groundwater, surface water and other potential water supplies have been considered sufficient to meet current and future annual demands (City of Stockton, 2007). The extended drought currently being experienced in California will likely cause reassessment of water supply, demand and management.

Five new storage tanks are needed to meet the required pressure for existing peak demands and fire flow conditions. The existing well pumping capacity is adequate, but 3 new wells are needed to improve the supply reliability during dry and critical years. The 10-inch diameter pipeline near Swain Road does not meet head loss and velocity requirements; a 12-inch diameter pipeline in parallel with the existing line is needed to meet standards. An 18-inch diameter looped pipeline system is required to improve the peakhour water pressure in the County Jail and Hospital area (City of Stockton, 2008a). With these improvements, the existing system will provide satisfactory service to Stockton.

Manteca and Lathrop
The Cities of Manteca and Lathrop rely on both surface and groundwater for their domestic water. Surface water became available in 2005 when the Nick C. DeGroot Water Treatment Plant began operation.

Manteca uses surface water to supplement groundwater from about April to October, when water use is high. The surface water used by both cities is from the Stanislaus River watershed.

Manteca has contracted to receive up to 11,500 acre feet/year from the South County Surface Water Supply Project, depending upon supplies available from the watershed. A planned expansion of the project would provide up to an additional 18,500 AF/year to Manteca. This would be sufficient surface water to support a doubling of the population to 150,000 residents. Groundwater is provided through a system of interconnected wells operated by the city. The wells range from 155 feet to 400 feet deep. Well capacity ranges from 380 gpm to 2,300 gpm. The city has a 300,000-gallon surface storage tank.

The City of Lathrop will receive up to 8,007 AF/year from the South County Water Supply Program. The City has two one million gallons storage tanks and one 425,000 gallons tank.

Waste Water
San Joaquin County
There are 9 publicly operated collection and treatment systems in the County, each associated with a city or town, including Stockton, Lathrop and Manteca. Some smaller, private treatment plants serve individual developments.

ATTACHMENT D 1358
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San Joaquin County, CA Affected Environment and Environmental Consequences Stockton
The city of Stockton’s wastewater is collected and treated by the Regional Wastewater Control Facility (RWCF) and the City of Stockton Wastewater Collection System Facilities. The City of Stockton Wastewater Collection System Facilities is a system of 965,289 feet of pipe and 28 pump stations that collect wastewater throughout the city for discharge to the RWCF or a downstream gravity sewer. RWCF is located north of Highway 4 on both sides of the SJR and provides primary, secondary and tertiary wastewater treatment (City of Stockton, 2007a). Under an NPDES permit, treated water from the RWCF is discharged into the SJR after dechlorination. Zero surface water discharge was considered, but found to be cost-prohibitive; the current plan for recycling is to use treated effluent to offset withdrawals of Delta water for potable use.

Between July 2008 and April 2013, RWCF exceeded final effluent limitations on several contaminants including ammonia, aluminum, cyanide and chlorine disinfection byproducts (CSWRCB, 2013). However, since immediate compliance is not practicable, the facility is following a time schedule order to ensure compliance by October 2013 which has subsequently been extended as improvements are made to the facility. RWCF met all interim effluent limitations outlined in the order (CVRWQCB, 2008) and the facility has increased monitoring, conducted impact studies, improved the disinfection facilities and constructed new nitrifying biotower facilities (City of Stockton, 2008b).

The RWCF has a dry-weather operational capacity of 55 million gallons per day (mgd) and currently processes an average of 33 mgd. Peak wet weather flows are projected to be 179.2 mgd. To meet future water quality permitting requirements and projected flows of 71 mgd average dry weather flow, 24,000 square feet of additional sedimentation basins, expansion of existing pumping and treatment facilities and expansion of secondary and tertiary treatment systems will be required by 2035 (City of Stockton, 2008b).

Manteca and Lathrop
The City of Manteca Wastewater Treatment Plant serves Manteca and Lathrop. It treats about 6.5 mgd of wastewater per day and has a capacity of 9.8 mgd. During the spring and summer, secondary effluent is applied agricultural fields and then discharged to the SJR. Dried sludge is spread on agricultural lands adjacent to the plant site.

The City of Lathrop contracts with Manteca for use of the Manteca Wastewater Treatment Plant. This facility treats wastewater generated in the areas east of Interstate 5 and north of Louise Avenue. All wastewater generated in the areas west of Interstate 5 and south of Louise Avenue is conveyed to the Lathrop Water Recycling Plant. This plant is designed to treat about 0.75 million gallons per day of raw sewage. The recycled water is used for landscape irrigation and farming activities for fodder crops.

Stormwater
The San Joaquin County Public Works Utilities Maintenance office maintains the stormwater system in the county. This system conveys stormwater directly to local waterways. The City of Stockton is responsible for stormwater collection, drainage and disposal and maintains and services all storm drains within the city limits. Primary waters that drain the city include: SJR, Bear Creek, Mosher Slough, Fivemile Slough, Fourteenmile Slough, Calaveras River and Stockton Diverting Canal, Smith Canal and French Camp and Walker Sloughs. Runoff in Lincoln Village west of Fourteenmile Slough is collected in the artificial lakes in the center of the development and pumped into the river when lake levels become too high. In other parts of Stockton, storm runoff is collected in 620 miles of underground pipes and pump stations that have adequate drainage capacity to serve existing and new development.

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San Joaquin County, CA Affected Environment and Environmental Consequences Municipal NPDES permitting, which involves management plans, treatment and monitoring of stormwater, is required because the City of Stockton qualifies as a large municipality. Stormwater discharges resulted in the classification of several waterways as “water quality impaired.” Waterways on the 303(d) list include Lower Calaveras River, Delta Waterways (eastern portion and Stockton Ship Channel), Mormon Slough, Mosher Slough and the SJR. Causes of impairment or threatened impairment include pesticides, heavy metals, pathogens and oxygen demanding substances (CVRWQCB, 2007).

In RD 17, stormwater is commonly collected in agricultural ditches, channels, stormwater sewers and retention ponds. The City of Stockton provides stormwater service to portions of RD 17. The City of Lathrop’s storm drainage system collects flows, stores them in detention basins and pumps them into the SJR through a municipal stormwater outfall. Stormwater in Manteca is handled by the city and by the South San Joaquin Irrigation District (City of Manteca, 2003). Drainage flows west into French Camp Canal, which flows into French Camp Slough and ultimately drains into the Delta. Manteca has a target level of service of 10-year storm drainage protection for all development and a 100-year storm drainage protection for all structures (City of Manteca, 2003).

Solid Waste
The County Solid Waste Management Plan governs solid waste management in all County jurisdictions.

The San Joaquin County Department of Public Works is responsible for solid waste management in the County. Most waste is municipal waste from residential and commercial/industrial sources. Three landfills serve the county: Foothill Sanitary Landfill, Lovelace Materials Recovery Facility and Transfer Station and North County Recycling Center and Sanitary Landfill.

Allied Waste, California Waste Recovery Systems and Waste Management are the 3 waste management companies that haul waste and provide recycling services for Stockton. About 67 percent of Stockton’s waste is diverted through curbside recycling, material recovery and composting. The remaining 33 percent is deposited in the landfill (CalRecycle, 2006). Stockton disposes of 229,000 tons of waste annually, with a per-capita daily disposal rate of 6.9 pounds (CalRecycle, 2011). In 1999, 46 percent of Stockton’s waste came from households and 54 percent came from businesses (CalRecycle, 1999).

Three landfills serve the city of Stockton, including Forward Landfill, Foothill Landfill and North County Sanitary Landfill. Foothill Landfill is the primary landfill, receiving an average of 810 tons per day and permitted for 1,500 tons per day. The Foothill Landfill has capacity until 2054 and there are no plans for new landfills or landfill expansion (City of Stockton, 2007).

In Manteca, the Manteca Solid Waste Division collects solid waste and deposits it at the Lovelace Solid Waste Transfer Station. Recyclable materials are sorted at the Lovelace facility. Green waste is delivered to the Austin Road/Forward Landfill, which has a capacity of 1,608,752 cy and a closure date of 2053 (City of Manteca, 2003).

Energy Use and Conservation
Pacific Gas and Electric Company (PG&E) supplies the study area, including Stockton, Manteca and Lathrop, with natural gas and electricity from the company’s inter-grid system. San Joaquin County consumes 5244 million kWh/year of electricity and 218 million therms of natural gas. Thirty-three (33) percent of the electricity and 44 percent of natural gas are consumed by residential users (CA Energy Commission, 2011).

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San Joaquin County, CA Affected Environment and Environmental Consequences Energy conservation efforts aim to appropriately site buildings for optimal sun exposure, implement active and passive solar heating and water systems, shade streets to reduce radiation heating and implement land use and transportation policies that encourage fewer and shorter vehicle trips. Stockton enforces the State (Title) 24 Building Codes on energy efficiency for all new development and also standard conditions for incorporation of solar energy conservation. Additional energy efficiency would be achieved by requiring that all new residential development meet the State Energy Star qualifications. Further, San Joaquin County and the City of Stockton are encouraging alternative energy sources such as landfill gas-to-energy facilities and solar energy.

Fire Protection
There are 41 fire departments and fire stations in San Joaquin County. These are all within existing urban communities. Fire protection in the unincorporated portion of the county is provided by rural fire districts or adjacent city fire departments. More remote areas are under the jurisdiction of the California Department of Forestry and Fire Protection (San Joaquin County, 2010).

The Stockton Fire Department serves the city and surrounding areas, including RD 17. The department has 80 emergency medical trained (EMT) personnel, 287 line suppression personnel, 38 civilian employees and twelve fire stations (City of Stockton, 2007). All the firefighters are certified as EMTs, with 111 firefighters certified to EMT-Paramedic level. The target response time is within 5 minutes.

RD 17 is served by the French Camp McKinley Fire District, which has one fire station located at 310 East French Camp Road in the town of French Camp and by the Lathrop-Manteca Fire Protection District, which has four fire stations placed throughout 100 square miles. The Lathrop-Manteca Fire Protection District serves the City of Lathrop and rural areas of Manteca and consists of: Fire Station 31, which is located at 800 East J Street in Lathrop; Fire Station 32, which is located at 22754 South Union Road in Manteca; Fire Station 33, which is located at 9121 East Lathrop Road in Manteca; and Fire Station 34, which is located at 460 River Islands Parkway (LMFD, 2010). The Lathrop-Manteca Fire District has a standard response time of 3 to 4 minutes (San Joaquin County LAFCo, 2009). The Manteca Fire Department serves the city of Manteca. There are three fire stations within the city limits. The Department also responds to medical emergencies. Their service standard is to maintain an average 5 minute response time for all emergencies (City of Manteca, 2003).

Police Services
San Joaquin County Sheriff Department provides law enforcement services for the unincorporated areas of the county. The Sheriff’s office also staffs a boating safety division. The County Sheriff department has 124 patrol officers that rotate shifts to provide law enforcement services 24 hours a day, 7 days per week (San Joaquin County 2009b). Stockton and Manteca each maintain a city police department. The Stockton Police Department currently has about 1 officer to 693 citizens and an emergency response time between three and five minutes (City of Stockton, 2007). The Manteca Police Department has a standard of one officer for every 1,000 residents. The Department has over 200 active volunteers who assist the Department and the community. The City of Lathrop Police Department includes 24 officers, 19 deputy sheriffs and four civilian staff members. The City of Lathrop contracts with the San Joaquin County Sheriff’s Department for law enforcement services and Lathrop police officers are San Joaquin County deputy sheriffs assigned to the City of Lathrop. San Joaquin County and the City of Lathrop have a flexible police staff agreement that accommodates modifications to service levels. Emergency response time within the core city is 2 to 4 minutes (San Joaquin County LAFCo, 2009).

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ASSESSMENT METHODS AND BASIS OF SIGNIFICANCE
Assessment Methods
This assessment is based upon a literature review and accepted standards of professional practice.

Basis of Significances
A project alternative would have a significant impact related to utilities and public services if it would:
 Result in substantial adverse physical impacts associated with the need for of new or physically altered public service or facilities, including police service, fire protection, school, library, drinking water, wastewater and stormwater collection facilities;  Substantially increase need for new or physically altered public service or facilities, the construction of which could cause significant environmental impacts, in order to maintain acceptable service ratios, response times or other performance objective;  Require new or expanded entitlements to provide sufficient water supplies to serve the project;  Require or result in the construction of new stormwater drainage facilities or expansion of existing facilities, the construction of which could cause significant environmental effects;  Require or result in the construction of new water or wastewater treatment facilities or expansion of existing facilities, the construction of which could cause significant environmental effects; or  Be served by a landfill with insufficient permitted capacity to accommodate the project’s solid waste disposal needs.

Effects and Mitigation Measures
The project would not involve any changes in land use that would increase short term or long term demand for public services, including fire and police protection, schools, parks and other public facilities, thus necessitating the construction of new or altered government service facilities. Similarly, the project would not result in demand for increased natural gas facilities, electrical transmission lines, communication systems, water infrastructure, sewer lines or solid waste facilities beyond their current capacity. These issues do not apply to this analysis and are not addressed further.

ALTERNATIVE 1 - NO ACTION
With implementation of Stockton’s General Plan, future growth would not exceed the capabilities or capacity of Stockton to provide utilities and public services, including police service, fire protection, schools, libraries or drinking water, wastewater and stormwater collection facilities.

Although anticipated growth would require improvement of public services and facilities, the impacts of induced development resulting from improved utilities and services would be mitigated to less than significant through implementation of City of Stockton policies and regulations.

Flooding that occurs under the No Action Alternative would result in backflow of stormwater facilities, including a 72-inch storm line which drains into Old Mormon Slough and storm drains for the subdivisions located south of Highway 120 in RD 17. Drainage pumping stations along the Calaveras River and along the north side of Smith Canal would remain below the 100-year flood elevation. Floodwaters would also exceed the pumping capacity of the Stockton Municipal Utilities District Waste Water Treatment plant, resulting in internal flooding of the plant and loss of service to over 300,000 customers (Emergency maps).

For floods which occur under the No Action Alternative, emergency actions would be required to protect California Water Service’s water supply system and East Bay Municipal Utility District’s aqueduct along ATTACHMENT D 1362
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San Joaquin County, CA Affected Environment and Environmental Consequences the north bank of the Calaveras River. The magnitude of the impact from levee failure would depend on the location of the levee breach, severity of the storm and river flows at the time of flooding. Predicting these events and providing a determination of significance is not possible based on the information available at this time. Therefore, identification of potential effects is too speculative for meaningful consideration.

ALTERNATIVE 7A
Project implementation would encroach on multiple types of utility equipment and facilities, including storm drains, irrigation lines, electric power lines and gas pipelines. Project construction activities, including grading and excavation, would require removal or reconnection of facilities and could damage identified and unidentified utility equipment and facilities. Substantial temporary interruptions of irrigation supply could occur if irrigation infrastructure is damaged or otherwise rendered inoperable at a time when it is needed (e.g., if reconnections to water supply sources are not completed by the time crop irrigation must begin). In addition, required relocation of existing electrical lines and gas pipelines could interrupt service. Design of the project would include consultation with all known service providers to identify infrastructure locations and appropriate protection measures and consultation would continue during construction to ensure that facilities are avoided and protected to minimize service disruptions as construction proceeds. Construction would not require the construction of new or expanded utility systems, including water supply facilities. Any connections to the municipal utility system would be coordinated with the appropriate utility provider prior to construction. The extent and intensity of project construction activities, however, may affect service providers’ abilities to quickly repair damage and/or restore interrupted service. This impact is considered significant. However, implementation of mitigation measures would reduce potential impacts to a less than significant levels.

ALTERNATIVE 7B
The footprint of Alternative 7b is greater than that of Alternative 7a, because it extends along the northern, western and southern levees of RD 17. The action and impacts of Alternative 7a are the same as Alternative 7b in North and Central Stockton, but would be greater because they also extend to RD 17. The extent and intensity of project construction activities may affect service providers’ abilities to quickly repair damage and/or restore interrupted service. This impact would be significant, but implementation of mitigation measures would reduce potential impacts to a less than significant level.

ALTERNATIVE 8A
The footprint of Alternative 8a is the same as the footprint of Alternative 7a, except that it extends further up Lower Calaveras River and along the Stockton Diverting Canal. The construction actions and impacts would be the same as those described for Alternative 7a, but would be greater because they extend further upstream on the Calaveras River and along the Stockton Diverting Canal. The extent and intensity of project construction activities may affect service providers’ abilities to quickly repair damage and/or restore interrupted service. This impact would be significant. However, implementation of mitigation measures would reduce potential impacts to a less than significant level.

ALTERNATIVE 8B
The footprint of Alternative 8b is the same as the footprint of Alternative 7a, except that it extends further up Lower Calaveras River and along the Stockton Diverting Canal and, like Alternative 7b, it includes construction work and impacts in RD 17. Therefore, the extent of construction activities and potential impacts are greater than those described for Alternative 7a and Alternative 7b. The extent and intensity of project construction activities may affect service providers’ abilities to quickly repair damage and/or restore ATTACHMENT D 1363
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San Joaquin County, CA Affected Environment and Environmental Consequences interrupted service. This impact would be significant. However, implementation of mitigation measures would reduce potential impacts to a less than significant level.

ALTERNATIVE 9A
The footprint of Alternative 9a is the same as the footprint of Alternative 7a, except that it includes a new flood bypass and channel improvements in Old Mormon Slough. In addition to the impacts described for Alternative 7a, a buried in-channel concrete box culvert constructed from Commerce Street to just upstream of Wilson Way collects much of the local drainage, including flows from 25 storm drains in this area. Under the channel improvements proposed in Alternative 9a, the culvert would be removed and the storm drains would be redirected to discharge directly into Mormon Channel. Therefore, the extent of construction activities and potential impacts are greater than those described for Alternative 7a. The extent and intensity of project construction activities may affect service providers’ abilities to quickly repair damage and/or restore interrupted service. This impact would be significant. However, implementation of mitigation measures would reduce potential impacts to a less than significant level.

ALTERNATIVE 9B
The footprint of Alternative 9b is the same as the footprint of Alternative 7a, except that it includes a bypass and channel improvements through Old Mormon Slough and, like Alternative 7b and 8b, it includes construction work and impacts in RD 17. In addition to the impacts described for Alternative 7a, 25 storm drains connect into a buried in-channel concrete box culvert upstream of Wilson Way on Old Mormon Slough. Under the channel improvements proposed in Alternative 9b, the culvert would be removed and the storm drains would be redirected to discharge directly into the Mormon Channel Bypass. The extent and intensity of project construction activities may affect service providers’ abilities to quickly repair damage and/or restore interrupted service. This impact would be significant. However, implementation of mitigation measures would reduce potential impacts to a less than significant level.

MITIGATION
Mitigation would be the same for all of the action alternatives. Before beginning construction, coordination with utility providers to implement orderly relocation of utilities that need to be removed or relocated would occur. Coordination would include the following:
 Notification of any potential interruptions in service shall be provided to the appropriate agencies and affected landowners.
 Before the start of construction, utility locations shall be verified through field surveys and the use of Underground Service Alert services. Any buried utility lines shall be clearly marked where construction activities would take place and on the construction specifications before of any earthmoving activities begin.
 Before the start of construction, the contractor would be required to coordinate with the local municipality and acquire any applicable permits prior to use of municipal water for construction.  Before the start of construction, a response plan shall be prepared to address potential accidental damage to a utility line. The plan shall identify chain of command rules for notification of authorities and appropriate actions and responsibilities to ensure the public and worker safety.

Worker education training in response to such situations shall be conducted by the contractor. The response plan shall be implemented by the contractor during construction activities.  Utility relocations shall be staged to minimize interruptions in service.

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San Joaquin County, CA Affected Environment and Environmental Consequences Implementation of this mitigation measure would reduce impacts caused by disruption of utility services under Alternatives 7a, 7b, 8a, 8b, 9a and 9b, to a less than significant level because the construction contractor would coordinate with service providers and consumers to minimize interruptions to the maximum extent feasible. A response plan to address service interruptions would be prepared and implemented.

RECREATION
This section describes the affected environment and environmental consequences relating to recreation for the LSJR project. The significance of the impacts and mitigation measures to reduce impacts are also discussed.

ENVIRONMENTAL SETTING
Regulatory Framework
No Federal, State, regional or local plan, policies, regulations, laws or ordinances related to recreation apply to the proposed LSJR project.

Existing Conditions
The City of Stockton maintains 63 parks, 106 miles of bicycle facilities and two public boat launch facilities.

San Joaquin County offers boating (one public boat launch in the project area), fishing and camping opportunities at 6 regional parks. Privately owned marinas, country clubs and golf courses provide additional recreational opportunities within the study area.

Three public boat launch facilities are located along project reaches: the Buckley Cove Boat Launch on the SJR north of the Calaveras; Louis Park Boat Launch at the confluence of Smith Canal; and Dos Reis Regional Park on the SJR north of Old River. The City-owned facilities provide day-use picnic areas and fishing opportunities; the county-owned Dos Reis Regional Park offers RV and tent camping in addition to day-use areas.

Waterways in the project area are used for recreational boating and fishing throughout the year. The private Village West Marina is located in northwest Stockton on Fourteenmile Slough, which is the primary waterway connecting the marina to the rest of the Delta and the SJR. Houseboats are present in Smith Canal.

Several existing Class I bike trails follow the alignment of Stockton’s waterways. The 6-mile bike trail along the north side of the Calaveras River and Stockton Diverting Canal provides an attractive corridor for cyclists. A bike trail also runs along the SJR between Henry Long Boulevard and Manthey Road (north and east along French Camp Slough). The city plans to increase bicycle facilities along Bear Creek, Mosher Slough, Old Mormon Slough and the SJR. The city plans to extend the existing bike path along the Calaveras River and to construct 5 bridges for pedestrians and cyclists (City of Stockton, 2007b).

Four golf and country clubs are located directly adjacent to project streams: Oakmore, adjacent to the Stockton Diverting Canal (this golf course is closed); Brookside, at the junction of the Calaveras River and the SJR; Stockton Golf and Country Club, adjacent to the SJR; and Van Buskirk along French Camp Slough.

ASSESSMENT METHODS AND BASIS OF SIGNIFICANCE
Assessment Methods
This assessment is based upon a literature review and accepted standards of professional practice.

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San Joaquin County, CA Affected Environment and Environmental Consequences Basis of Significance
The proposed project would have a significant impact on recreational resources if it would:
 Increase the use of existing neighborhood and regional parks or other recreational facilities, such that substantial physical deterioration of the facility would occur or be accelerated; or  Would result in substantial adverse physical impacts associated with the need for new or physically altered parks or recreational facilities.

ALTERNATIVE 1 - NO ACTION
Stockton offers recreational opportunities through public parks and would be able to maintain sufficient recreational area to population ratios to meet future needs for recreational opportunities without adversely impacting other resources. Boating opportunities would not be adversely impacted. Following the Stockton General Plan (2007), bicycle paths along the Calaveras River, Bear Creek, Mosher Slough, the Stockton Channel, Mormon Slough and SJR would be developed by 2035.

If a flood event were to occur, park facilities could be covered with sediment and the facilities could be damaged. Additionally, bike paths and running trails which are adjacent to the levee would likely be damaged and unusable for an extended period of time. The magnitude of the impact resulting from levee failure would depend on the location of the levee breach, severity of the storm and river flows at the time of flooding. Predicting these events and providing a determination of significance is not possible based on the information available at this time. Therefore identification of potential effects is too speculative for meaningful consideration.

ALTERNATIVE 7A
Implementation of Alternative 7a would temporarily disrupt recreational activities on and along the Calaveras River and SJR and at Louis Park. Construction activities such as grading, removing vegetation, trenching, constructing cutoff walls and placing seepage berms would affect the scenery and thus passive recreational activities (e.g., walking, photography, bird watching). Most impacts would be temporary because construction-related equipment that would be visible from recreational facilities (i.e., open space and Calaveras and SJRs) would be removed after completion of construction activities.

In addition, recreational access to Dad’s Point on Smith Canal would be closed for two to three construction seasons. The Buckley Cove, Louis Park and Dos Reis Park parking lots could be used for staging of materials and equipment, potentially affecting use of the boat ramps and disrupting passive recreational opportunities for two to three construction seasons. Three additional public boat launches, including the Morelli Park Boat Launch, would be available to access the SJR during any closures.

The gate structures across Smith Canal and Fourteenmile Slough would each have a 50 foot opening for boat passage and would be exercised (i.e., closed and immediately opened) once or twice a year. Gate operations and the conditions, frequency and duration of gate closures are described in Section 4.5.6.

Operation of the closure structures would be relatively infrequent except during January and February high tides (8.0 ft+) when the gates would close up to 10 times per month and remain closed for a few hours up to 24 hours. Gates would be closed for short durations except during flood events which would be expected to occur about every 2 to 3 years. When flood events together with high tides occur, the gates could remain closed from a few days to a few weeks. Therefore, these closure structures would not have significant permanent impacts to recreation.

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San Joaquin County, CA Affected Environment and Environmental Consequences During construction, the SJR would be inaccessible from the Louis Park boat launch and docks along the Smith Canal for half a year as the closure structure and dual sheetpile wall are completed. Similarly, Fourteenmile Slough would also be inaccessible for about half a year from Fivemile Slough westward to where Fourteenmile bifurcates around Rindge Tract. This would disrupt access to the Delta for boaters traveling into and out of Village West Marina.

The waterways in the project area would remain accessible; however, there would be temporary impacts to boating and recreational opportunities which would be short term to those along the Smith Canal and Fourteenmile Slough. Similarly, once construction is complete, boaters, including those using the Village West Marina, would have access to the SJR and Fourteenmile Slough.

The construction of Alternative 7a would require extensive work on the levee crown, which would disrupt bicycling and jogging along the Calaveras River Bike trail and the SJR Bike Trail. Detours would likely be required along 3 miles of bike trail during each 5-month construction season in these reaches. Impacts would be temporary because the bike trails would be restored after construction is complete.

Implementation of Alternative 7a would not affect the City’s long term plans to improve and extend the existing bicycle network. Impacts to recreation, to boating opportunities and bicycle paths would be less than significant.

Removal of trees and shrubs to construct structural project features and to establish compliance with the Vegetation ETL could adversely affect the recreational experience by changing the view-shed and the microclimate (i.e., reducing the amount of shade available). Vegetation removal would also reduce habitat for wildlife, such as birds, thereby reducing their presence on or adjacent to the levees in the project area.

There are many recreation facilities in the study area that would not be affected by project construction and would continue to provide recreation opportunities. Detour routes and alternative access would allow recreation activities to continue during the construction season. The project would not generate the need for additional recreation facilities or generate additional recreation needs.

Although a limited number of people would be affected by the project and additional recreational facilities would not be required as a result of the project, the effects to recreation would be significant and unavoidable because of short and long term impacts to the visual quality of the experience, reduced shade and reduced opportunity for bird watching and wildlife viewing.

ALTERNATIVE 7B
Implementing Alternative 7b would have the same recreation impacts as Alternative 7a in North and Central Stockton. In addition, implementing Alternative 7b would temporarily disrupt recreational activities on and along the SJR adjacent to RD 17; at Mossdale County Park; and in the open spaces in RD 17. As for Alternative 7a, most impacts would be temporary because construction-related equipment that would be visible from recreational facilities (i.e., open space and Mossdale County Parks, Calaveras and SJRs) would be removed after completion of construction activities.

Impacts to recreation resulting from construction of the gate structure across Smith Canal would be the same as those described for Alternative 7a. The waterways in the project area would remain accessible; however, there would be temporary impacts to boating and recreational opportunities which would be short term to those along the Smith Canal.

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San Joaquin County, CA Affected Environment and Environmental Consequences The construction of Alternative 7b would require extensive work on the levee crown, which would disrupt bicycling, walking and jogging along the Calaveras River Bike trail and the SJR Bike Trail; detours would likely be required along 3 miles of bike trail during each 5-month construction season in these reaches.

Impacts would be temporary because the bike trails would be restored after construction is complete.

Implementation of Alternative 7b would not affect the city’s long-term plans to improve and extend the existing bicycle network.

There are many recreation facilities in the study area that would not be affected by project construction and continue to provide recreation opportunities. Detour routes and alternative access would allow recreation activities to continue during the construction season. The project would not generate the need for additional recreation facilities or generate additional recreation needs. However, there would impacts to visual quality, reduced shade and wildlife viewing opportunities would extend throughout the project area in RD 17. These impacts would be significant and unavoidable in both the short and long-term.

ALTERNATIVE 8A
Alternative 8a would include the same project impacts as those in Alternative 7a, but would also include additional construction along portions of the Lower Calaveras River and the Stockton Diverting Canal. The Stockton Diverting Canal and the additional portions of the Lower Calaveras River that are included have few trees and shrubs to contribute to the recreational experience. Affects to recreation from implementing Alternative 8a would be significant and unavoidable because of short and long term impacts to the visual quality of the experience, reduced shade and reduced opportunity for bird watching and wildlife viewing.

ALTERNATIVE 8B
Implementation of Alternative 8b would result in the same recreation impacts as Alternative 7b, except Alternative 8b includes additional levee improvements along the Upper Calaveras River and on the Stockton Diverting Canals. Alternative 8b would temporarily disrupt recreational activities on and along the Calaveras River and SJR; at Louis Park and Mossdale County Park; and in the open spaces in RD 17.

The types of impacts are consistent with the descriptions under Alternative 7b.

The waterways in the project area would remain accessible; however, there would be temporary impacts to boating and recreational opportunities which would be short term to those along the Smith Canal and Fourteenmile Slough. Similarly, once construction is complete, boaters, including those using the Village West Marina would have access to the SJR and Fourteenmile Slough.

The construction of Alternative 8b would require extensive work on the levee crown, which would disrupt cycling and jogging along the Calaveras River Bike trail and the SJR Bike Trail; detours would likely be required along 3 miles of bike trail during each 5-month construction season in these reaches. Impacts would be temporary, because the bike trails would be restored after construction is complete.

Implementation of Alternative 8b would not affect the city’s long-term plans to improve and extend the existing bicycle network.

Although a limited number of people would be affected by the project and additional recreational facilities would not be required as a result of the project, the affects to recreation would be potentially significant and unavoidable because of short term and long term impacts to the visual quality of the experience, reduced shade and reduced opportunity for bird watching and wildlife viewing.

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San Joaquin County, CA Affected Environment and Environmental Consequences ALTERNATIVE 9A
Alternative 9a would consist of the same repairs along the same linear extent as described for Alternative 7a, with the exception that Alternative 9a also includes improvements to Old Mormon Slough. This abandoned channel is not currently open to the public. The proposed channel improvements would allow for future development of walking trails, which could increase passive recreational opportunities. Although recreational improvements are not planned as a part of this project and would thus be too speculative for a precise determination of impact, permanent impacts in the Old Mormon Slough are expected to be positive or less than significant.

For the reasons described for Alternative 7a, Alternative 9a would result in affects to recreation would be potentially significant and unavoidable because of short and long term impacts to the visual quality of the experience, reduced shade and reduced opportunity for bird watching and wildlife viewing.

ALTERNATIVE 9B
Alternative 9b would consist of the same repairs along the same linear extent as Alternative 7b, with the exception that Alternative 9b also includes improvements to Old Mormon Slough, making it into the Mormon Channel flood bypass. This old slough is not currently open to the public; the proposed channel improvements would allow for future development of walking trails, which could increase passive recreational opportunities. Although recreational improvements are not planned as a part of this project and would thus be too speculative for a precise determination of impact, permanent impacts in the Old Mormon Slough are expected to be positive or less than significant.

For the reasons described for Alternative 7b, the affects to recreation would be potentially significant and unavoidable because of short and long term impacts to the visual quality of the experience, reduced shade and reduced opportunity for bird watching and wildlife viewing.

MITIGATION
Detours and alternative recreation locations would provide sufficient recreation opportunities in the study area. Impacts resulting from the loss of vegetation would be mitigated on site, where feasible, through additional plantings in existing parks. Approaches to mitigate for loss of vegetation are in Section 5.9.

Implementing these measures would reduce impacts to recreation that are associated with vegetation.

However, impacts to the recreational experience due to vegetation removal and the resulting changes in the visual quality, shade and reduced opportunities for bird watching and wildlife viewing would remain significant and unavoidable.

AESTHETICS
This section describes the affected environment and environmental consequences relating to aesthetics for the LSJR project and the significance of the impacts and mitigation measures to reduce impacts.

ENVIRONMENTAL SETTING
Regulatory Framework
No Federal, State, regional or local plans, policies, regulations or laws related to aesthetics apply to the proposed LSJR project.

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San Joaquin County, CA Affected Environment and Environmental Consequences Existing Conditions
An area's visual character is determined by the variety of visual features present, the quality of those features and the scope and scale of the scene. The visual components of a particular area consist of such features as landforms, vegetation, man-made structures and land use patterns. The quality of these features depends on the relationship between them and their scale in the overall scene.

In assessing the aesthetic effects of a project, the visual sensitivity of the site must be considered. Areas of high visual sensitivity are easily visible to the general public. Scenic highways, tourist routes and recreation areas generate sensory reactions and evaluations by the observer. The evaluations of a particular scene will vary depending on the perceptions and values of the observer. The determination of significance of potential aesthetic effects is based on the change in visual character as determined by the obstruction of a public view, creation of an aesthetically offensive public view or adverse changes to objects having aesthetic significance.

The North and Central Stockton portions of the project area consist of a diverse range of urban settings, with potential observers ranging from homeowners to passing joggers. In some residential areas, homeowners’ properties extend up and over the levee and vary from well-landscaped backyards to weedy lots. Many homeowners in these reaches set out umbrellas and chairs to enjoy the peaceful waterfront views (Figure 5-19).

Figure 5-19: Residential Levee with Waterfront Views (Fourteenmile Slough) In areas where public levee access is permitted, the streams provide an important visual amenity to joggers and passersby, contrasting with the neatly laid-out residential parcels in rows on the landside of the levee.

Reaches with riparian vegetation and wildlife add visual heterogeneity and dynamic qualities to the otherwise barren levees. Graffiti and trash detract from the aesthetics of non-residential areas, particularly trash in the Old Mormon Slough (Figure 5-20) and graffiti on the Calaveras River floodwall.

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San Joaquin County, CA Affected Environment and Environmental Consequences Figure 5-20: Old Mormon Slough
Views in the RD 17 portion of the Project Area are characterized by the SJR, adjoining waterways and the existing dry land levee. The visual characteristics of RD 17 contrast starkly with the urban setting of North and Central Stockton. These reaches are rural, dominated by row cropping and orchards on the landside.

The higher variety of waterside vegetation in these reaches adds to the visual appeal, although there are fewer potential observers due to restrictions on public access and lower population density in the area.

Sensitive viewers include nearby residents and farmers, motorists and people recreating at parks and open spaces along the levee system.

ASSESSMENT METHODS AND BASIS OF SIGNIFICANCE
Assessment Methods
This assessment is based upon a literature and accepted standards of professional practice.

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San Joaquin County, CA Affected Environment and Environmental Consequences Basis of Significance
The implementation of the proposed project would have a significant impact on visual and aesthetic quality if it would:
 Substantially or demonstrably result in a negative aesthetic alteration to the existing character of the area. A substantial alteration is characterized by a negative “sense of loss” of character or unique resources;
 Have a substantial adverse effect on a scenic vista; or  Create a new source of substantial light or glare which would adversely affect daytime or nighttime views in the area.

ALTERNATIVE 1 - NO ACTION
Features that define the character of the area identified by the Stockton General Plan (2007include open space areas, agricultural fields and riparian areas in addition to residential communities and commercial development. Depending on climate conditions, residents of Stockton can view the Coastal Range and the Sierra in the distance. As Stockton grows, land use changes and air quality impacts associated with development are likely to impact some of these features. The General Plan contains policies that work in conjunction with current city design and development regulations to ensure that new development complements the existing aesthetic fabric of city of Stockton and its surrounding environment and does not threaten scenic corridors. Even with mitigation measures, however, the development outlined in the General Plan would create new sources of light and glare.

Under the No Action Alternative, a substantial risk of flooding would remain. Flooding resulting either from a localized levee failure or simultaneous levee failures in more than 1 location in the levee system, could cause damage to structures. The No Action Alternative could have a significant effect on the character of the residential and commercial areas depending on the extent and duration of flooding and subsequent repair. Construction would be required to repair flood damage, resulting in the presence and movement of heavy construction equipment and potential temporary sources of light and glare.

Future flooding would not degrade the physical appearance of features which contribute to scenic vistas, including farmlands, open space and riparian habitats along the SJR and tributaries. Although farmlands are functionally impacted following flooding, they remain open spaces and continue to contribute to the rural quality of views. Similarly, riparian habitats may be damaged, but would retain the undeveloped appearance which contributes to the scenic views. Flooding does not affect light or glare. Therefore, impacts on aesthetics would be less than significant.

ALTERNATIVE 7A
Installation of the closure structure at Smith Canal would result in a large wall across most of the opening.

The wall would degrade the physical appearance of open water features which contribute to scenic vistas.

Additionally, the floodwall along Dad’s Point would become a physical barrier to the view of the open waters from the park area and some homes.

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San Joaquin County, CA Affected Environment and Environmental Consequences Project improvements with full vegetation removal would not create any new sources of light or glare.

However, removal of trees and shrubs would reduce shade and expose the area to sunlight throughout the day and to glare and light at sunrise and sunset. Complete removal of waterside vegetation would also alter the experience and the quality of views for nearby sensitive receptors. Vegetation removal would greatly reduce or eliminate riparian habitat, which contributes to scenic vistas and the existing visual character of the site. Post project foreground views would be drastically different from pre-project foreground views.

Since no mitigation would be feasible for the complete removal of waterside vegetation or from effects on views from the Smith Canal and floodwall, these impacts would be permanent, significant and unavoidable.

ALTERNATIVE 7B
Visual impacts under Alternative 7b would be similar in nature but greater in extent than those described for Alternative 7a. The increase in extent results from construction that would occur along the northern, western and southern levees in RD 17. Since no mitigation would be feasible for the complete removal of waterside vegetation, these impacts would be permanent, significant and unavoidable.

ALTERNATIVE 8A
Visual impacts described for Alternative 7a would be the same as Alternative 8a at the Smith Canal closure structure and Dad’s Point, as would impacts with vegetation removal. Since no mitigation would be feasible for the complete removal of waterside vegetation, these impacts would be permanent, significant and unavoidable.

ALTERNATIVE 8B
Visual impacts described for Alternative 7a above would be the same for Alternative 8b at the Smith Canal closure structure and Dad’s Point, as would impacts with vegetation removal. Since no mitigation would be feasible for the complete removal of waterside vegetation, these impacts would be permanent, significant and unavoidable.

ALTERNATIVE 9A
Visual impacts under Alternative 9a would be the same as those described for Alternative 7a except that the visual landscape will change on Old Mormon Slough as a result of converting it into a flood bypass.

Since no mitigation would be feasible for the complete removal of waterside vegetation, these impacts would be permanent, significant and unavoidable.

ALTERNATIVE 9B
Visual impacts described for Alternative 7b would be the same for Alternative 9b at the Smith Canal closure structure and Dad’s Point, as would impacts with vegetation removal. Since no mitigation would be feasible for the complete removal of waterside vegetation, these impacts would be permanent, significant and unavoidable.

MITIGATION
No mitigation is feasible for the Smith Canal closure structure and the wall along Dad’s Point. USACE would seek opportunities during the design phase of the project to plant onsite vegetation, if a variance is received, which would reduce impacts to aesthetics. However, impacts from compliance with the Vegetation ETL would remain significant and unavoidable.

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San Joaquin County, CA Affected Environment and Environmental Consequences NOISE
This section describes the affected environment and environmental consequences relating to noise for the LSJR project. The significance of the impacts and mitigation measures to reduce impacts are also discussed.

ENVIRONMENTAL SETTING
Regulatory Framework
Laws, regulations and requirements that apply to noise are listed below and summarized in Chapter 7, Compliance with Applicable Laws, Policies and Plans.

Federal
 Executive Order 11988, Floodplain Management
 Noise Control Act (42 USC §§ 4901-4918)
State
 California Code of Regulations, Title 24
 State of California General Plan Guidelines (OPR 2003) Local
 California Land Conservation Act of 1965 (Williamson Act)  City of Manteca General Plan 2003 (Goal N-I; Goal N-4, Policy N-P-1, Policy N-P-4, Policy N-P5, Policy N-P-7; Implementation N-I-3; Implementation N-I-4  City of Manteca Zoning Ordinance, Manteca Municipal Code 2003 – Title 17-Zoning  Comprehensive General Plan for the City of Lathrop, California (City of Lathrop 2004)  City of Stockton General Plan (2007)
 San Joaquin County Plan (2010)
Existing Conditions
North and Central Stockton portions of the project area are primarily urban, with a mix of residential and industrial land uses. RD 17 is a rural, predominantly agricultural area and is relatively quiet. The primary sources of noise in North and Central Stockton include traffic along I-5, State Route 99 and several local roadways, intermittent trains and the Port of Stockton’s loading operations along the Stockton Deep Water Ship Channel. Ambient sounds in RD 17 include birds and distant traffic. Farming operations and intermittent trains are the primary sources of noise greater than ambient conditions in RD 17.

Noise varies over time, as background noise gradually increases and decreases throughout the day and as short term noise events such as sirens or passing aircraft are added to the ambient noise levels. Thresholds for noise exposure are normally expressed with statistical noise descriptors such as an average daily exposure level over an extended period of time or average day-night sound level (Ldn). To account for greater noise sensitivity during evening hours, nighttime noise exposure is more heavily weighted than daytime exposure in the calculation of Ldn. Short term noise levels measured over a brief period are expressed as Leq. Sound intensity is measured in decibels (dB). Because the intensity of noise does not increase linearly with increasing dB, noise levels are often expressed using the A-scale (dBA), so that a doubling of dBA represents a doubling of intensity. The EPA has defined 55 DBA Ldn as the goal for residential environments (USEPA, 1974).

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San Joaquin County, CA Affected Environment and Environmental Consequences The City of Stockton measured ambient noise levels throughout the city during the development of the 2007 General Plan. A short term (10-15 minute) noise measurement was taken in Sandman Park on the north side of Mosher Slough. Estimated typical Ldn (day-night average sound level) for this location was 61 dB, with a maximum sound level of 94 dB (Background Report). Ldn generated by vehicle traffic along I-5 and SR-99 and railroad traffic along the Union Pacific Railroad (UPRR) and Burlington Northern Santa Fe (BNSF) dominate the noise environment where these routes cross the project reaches.

Railroads cross the project area in several locations including the Calaveras River, Stockton Diverting Canal, SJR and Old Mormon Slough. The operations include both freight and passenger service and about half occur between 7 a.m. and 10 p.m. UPRR operates a total of 43 trains per day and BNSF operates 50 trains per day. Without warning horns, the approximate Ldn 424 feet from the tracks is 65 dB. With warning horns, the noise 414 feet from the tracks increases to 70 dB.

Table 5-38: Approximate Distances to UPRR Noise Contours

ASSESSMENT METHODS AND BASIS OF SIGNIFICANCE
Assessment Methods
This assessment is based upon a literature review and accepted standards of professional practice.

Basis of Significance
Implementation of a project alternative would result in a significant noise impact if it would:
 Expose people to or generate noise levels in excess of, standards established in the local general plan, noise ordinance or applicable standards of other agencies;  Expose people to or generate excessive groundborne vibration or groundborne noise levels;  Result in a substantial permanent increase in ambient noise levels in the project vicinity above levels existing without the project;
 Result in a substantial temporary or periodic increase in ambient noise levels in the project vicinity above levels existing without the project; or
 Result in the encroachment of incompatible land uses near known noise producing industries, railroads, airports and other sources.

The proposed project would not modify the existing or planned land use and would not be located in the vicinity of any public or private airports; therefore, none of the proposed alternatives would result in the encroachment of incompatible land uses near known noise-producing sources. Future O&M of the project levees would require regular control of all vegetation on and adjacent to the levees. The equipment required for this maintenance would be similar to what is currently used. Therefore, none of the proposed alternatives would result in a substantial permanent increase in ambient noise levels. These effects will not be discussed in further detail.

Ldn Noise Level (dB) Distance to Noise Contour with
warning horns (feet)
Distance to Noise Contour
without warning horns (feet)

60.0 1,969 914

65.0 914 424

70.0 424 197
(Source: Draft EIR for Stockton General Plan, pg 11-1)
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The Federal Transit Administration (FTA) issued guidance for noise and vibration impact assessment of Federally-funded mass transit projects (FTA, 2006). Although specifically intended for construction of mass transit projects, the FTA guidelines will be used as a threshold of potential significance for the proposed project. The impact criteria are listed in Figure 5-21 for noise and Table 5-39 for vibration.

Figure 5-21: Noise Impact Criteria for Transit Projects (FTA 2006) Depending on the existing noise levels at the receptor, FTA noise impact thresholds range from 50 dB Leq to 65 dB Leq for Land Use Categories 1 and 2 and 55 dB Leq to 70 dB Leq for Land Use Category 3. Land Use Category 1 includes lands set aside for serenity and quiet, such as recording studios, outdoor amphitheaters and concert pavilions; as well as National Historic Landmarks. Land Use Category 2 includes buildings where people normally sleep and where nighttime sensitivity to noise is high, such as homes and hospitals. Land Use Category 3 includes institutional land uses with primarily daytime and evening use such as schools, libraries and churches.

Vibration is an oscillatory motion that is measured in vibration decibels (VdB). The effects of vibration can include movement in floors and rattling of windows and items on shelves and other surfaces. It can also include sensations detectable in the bodies of humans and other animals. The magnitude, frequency and duration of exposure to vibration all contribute to the impacts of vibration. Vibration in the range of 50 VdB to 100 VdB is of interest. Humans typically perceive vibration when it reaches 65 VdB, but vibration levels do not become bothersome until they exceed 70 VdB (FTA, 2006).

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San Joaquin County, CA Affected Environment and Environmental Consequences Vibration thresholds range from 65 VdB to 83 VdB depending on the event frequency and the land use category (Table 5-39). “Frequent events” are defined as more than 70 vibration events of the same source per day. “Occasional events” are defined as between 30 and 70 vibration events of the same source per day. “Infrequent events” are defined as fewer than 30 vibration events of the same kind per day. Land use Category 1 includes buildings where vibration would interfere with interior operations. The vibration threshold for this category is 65 Vdb. Category 2 includes residences and buildings where people normally sleep. The vibration threshold for this category is 72 VdB for frequent events, 75 VdB for occasional events and 80 VdB for infrequent events. Category 3 includes institutional land uses with primarily daytime use.

The vibration threshold for this category is 75 VdB for frequent events, 78 VdB for occasional events and 83 VdB for infrequent events. Receptors with primarily daytime use or which experience relatively infrequent vibration events have higher annoyance thresholds (65-83 VdB) than receptors with nighttime use and/or frequent vibration events (65-75 VdB).

Table 5-39: FTA Groundborne Vibration Impact Criteria for General Assessment Land Use Category
GBV Impact Levels
(VdB re 1 micro-inch/sec)
Frequent
Events1
Occasional
Events2
Infrequent
Events3
Category 1: Buildings where vibration
would interfere with interior operations 65 VdB 65 VdB 65 VdB Category 2: Residences and Buildings
where people normally sleep 72 VdB 75 VdB 80 VdB
Category 3: Institutional Land uses
with primarily daytime use 75 VdB 78 VdB 83 VdB
Notes:

1. "Frequent Events" is defined as more than 70 vibration events of the same source per day.

2. “Occasional Events” is defined as between 30 and 70 vibration events of the same source per day.

3. "Infrequent Events" is defined as fewer than 30 vibration events of the same kind per day.

Source: FTA, 2006. Transit Noise and Vibration Impact Assessment State
State of California General Plan Guidelines
The Governor’s Office of Planning and Research (OPR) published the State of California General Plan Guidelines (OPR, 2003), which provides guidance for the acceptability of projects within specific day-night average noise level (Ldn) contours. Generally, residential uses (e.g., mobile homes) are considered to be acceptable in areas where exterior noise levels do not exceed 60 A-weighted decibels (dBA) Ldn.

Residential uses are normally unacceptable in areas exceeding 70 dBA Ldn and conditionally acceptable within 55–70 dBA Ldn. Schools are normally acceptable in areas up to 70 dBA Ldn and normally unacceptable in areas exceeding 70 dBA Ldn. Commercial uses are normally acceptable in areas with a community noise equivalent level (CNEL) of up to 70 dBA. Commercial uses are conditionally acceptable where the Ldn is between 67.5 and 77.5 dBA, depending on the noise insulation features of the building and the noise reduction requirements in the facility design. The OPR guidelines also provide adjustment factors for determining noise acceptability standards that reflect the noise control goals of the community, the particular community’s sensitivity to noise and the community’s assessment of the relative importance of noise pollution.

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San Joaquin County, CA Affected Environment and Environmental Consequences California Code of Regulations, Title 24
Title 24 of the California Code of Regulations establishes standards for interior noise levels that apply to all new, multifamily residential units. These standards require that acoustical studies be performed before construction begins at locations where the existing Ldn exceeds 60 dBA. Such acoustical studies are required to establish mitigation measures that limit maximum Ldn levels to 45 dBA in any habitable room.

Although no interior noise standards are pertinent to all uses, many communities have adopted an Ldn of 45 dBA as an upper limit on interior noise in all residential units.

Local Criteria
Noise standards were established through general plans and noise ordinances for San Joaquin County, Manteca, Stockton and Lathrop. San Joaquin County Municipal Code (Section 9-1025.9[c][3]) specifically exempts construction activity occurring between 6:00 am and 9:00 pm on any day. Manteca Municipal Code (Section 17.058.050[d][8]) exempts construction conducted between 7:00 am and 7:00 pm as a part of an approved building permit. Stockton and Lathrop do not specifically exempt construction activities and review construction plans to determine whether the proposed project complies with the local ordinances. The City of Stockton General Plan states that “the City shall limit construction activities to the hours of 7am to 7pm, Monday through Saturday. No construction shall occur on Sundays or national holidays without a written permit from the City” and that “the City shall seek to limit the potential noise impacts of construction activities on surrounding land uses.” Although daytime construction noise may be exempt in some locations, exterior noise exposure criteria for Stockton, Lathrop, Manteca and San Joaquin County are presented as a means for determining potential significance (Table 5-40).

Table 5-40: Exterior Noise Exposure Criteria Applied to Stationary Noise Sources at Residential Receivers
Noise Level
Descriptor
City of
Stockton
City of
Manteca
City of
Lathrop
San Joaquin
County
Day Night Day Night Day Night
Leq 55 45 50 45 -- -- 50 45
Lmax 75 65 70 65 75 65 70 65
Sources: Stockton Municipal Code Section 16-60.040[b], San Joaquin County Municipal Code Section 9-1025.9[c][3], Manteca General Plan (2003), Lathrop General Plan (1991)
Other Considerations
Construction equipment and activities cause vibration. Some activities, like pile driving, can cause sharp and dramatic hydrostatic pressure waves and vibrations that can adversely affect all life stages of fish over relatively long distances (Washington et al. 1992). Hydrostatic pressure waves could rupture the swim bladders and other internal organs of all life stages of fish in the immediate construction area (Bonneville Power Administration 2002; Jones & Stokes Associates 2001; Washington et al. 1992). Additionally, noise and vibration generated by pile driving activities could have sublethal effects on individual fish by inciting movement into lower quality habitats (Bonneville Power Administration, 2002).

There is evidence that lethal effects can occur from pile driving, but accurately analyzing and addressing these, as well as sublethal effects (e.g., injury, temporary hearing threshold shifts, stress and behavioral disturbance) is complicated by several factors. Sound levels and particle motion produced from pile driving can vary depending on pile type and size, substrate composition and type of equipment used. Also, the effects of underwater noise vary among species as a function of species morphology and species ATTACHMENT D 1378
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San Joaquin County, CA Affected Environment and Environmental Consequences physiology. Further Oriard (1985) and Jones & Stokes Associates (2001) noted that the effects of energy resulting from blasting in rock adjacent to waterways differs depending on the composition and slope of the bank and specifically is reduced relative to in-water blasting. Presumably, pile driving activities on land result in similar reductions in energy transfer to waterways and thus would result in lesser effects than inriver activities. Therefore, the effects assessment qualitatively evaluates whether the project alternative would be anticipated to change conditions in the SJR, Stockton Deep Water Ship Channel, Smith Canal and/or the Delta sloughs in the project area as a result of hydrostatic pressure waves and increased noise and vibration caused by construction along the levee, floodwall and gate footprints.

ALTERNATIVE 1 - NO ACTION
Under the No Action Alternative, the current level of risk for a major levee failure and flooding within the project area would remain. In the event of a levee breach, repair-related construction activities would occur.

The location and extent of repair-related activities could be minor to extensive depending on the location and severity of the levee failure and duration of flooding. Repair-related construction activities would likely involve repairing damaged homes, utility infrastructure, roads and highways. Noise-sensitive land uses (i.e., residential uses) are dense throughout the area in which repair-related construction could be needed. Levee failure would likely result in evacuation of people (i.e., sensitive receptors) until levee repairs were completed. Without these sensitive receptors present, potential impacts related to temporary and short term construction noise and groundborne vibration associated with levee repair would not be anticipated and the impact would be less than significant.

ALTERNATIVE 7A
Construction of levee improvements under Alternative 7a would generate short-term and intermittent noise and vibration at or near individual noise- and vibration-sensitive locations along 23.6 miles of project reaches.

Noise
Construction activities associated with slurry cutoff walls would proceed in a linear manner, with noise levels of 50 dB Leq or above affecting individual residences for up to 4 weeks in most locations. Activities associated with deep-soil mixing would also proceed in a linear fashion but more slowly, with noise levels of 50 dB Leq or above affecting residences for 2 to 4 years depending on the number of rigs used.

Construction activities associated with levee widening and levee raises would involve recurring construction activities along the entire length of the site until construction is complete. On site equipment required for construction activities would include excavators, backhoes, bulldozers, scrapers, rollers, graders, loaders, compactors, pile drivers and various trucks.

Noise levels would fluctuate depending on the physical location of construction activities and on the type, number and duration of use of various construction equipment. Maximum noise levels produced by individual equipment during these operations could range from 80 to 90 dBA without the implementation of feasible noise control and at a distance of 50 feet from the nearest noise source, as indicated in Table 5-41. Construction noise attributable to the project was estimated using the FTA noise methodology for the prediction of the cumulative noise level generated by the three loudest pieces of equipment operating simultaneously (FTA, 2006). Table 5-42 shows the results for the various stages of construction activities for all alternatives, based on equipment requirements for construction listed in Chapter 4, Description of Final Alternatives. All results assume no intervening barriers.

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San Joaquin County, CA Affected Environment and Environmental Consequences Table 5-41: Typical Maximum Noise Level for Construction Equipment Equipment Type
Typical Maximum Noise Level in
dBA at 50 Feet
Dump Truck 88
Loader 86
Dozer 84
Grader 85
Vibratory Roller 82
Backhoe 85
Chain Trencher 85
Spreader 88
Paver 89
Water Truck 88
Backhoe/Skiploader 86
Pickup Truck 67
Forklift 86
Compactor 89
Pile Driver 1011
Concrete Truck 88
Concrete Pump 82
Deliver Truck 80
Crane 83 1 FHA, Construction Noise Handbook,
http://www.fhwa.dot.gov/environment/noise/construction_noise/handbook/handbook09.cfm Table 5-42: Predicted Noise Levels Due to Major Construction Activities for All Alternatives Action
Resulting noise
level in dBA Leq
at 100 feet
Distance to noise contour (Feet)
40 dBA
Leq
45 dBA
Leq
50 dBA
Leq
55 dBA
Leq
Clearing and
grubbing/stripping 77.8 2750 1770 1147 740
Removal of landside
structures and facilities 77.8 2750 1770 1147 740
Cutoff Wall Construction 77.8 2750 1770 1147 740
Seismic Deep Soil Mixing 77.8 2750 1770 1147 740
Seepage Berm Construction 77.8 2750 1770 1147 740
Closure Structure
Construction 81.5 3802 2454 1584 1020
Restoration/
Demobilization 77.8 2750 1770 1147 740
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San Joaquin County, CA Affected Environment and Environmental Consequences Residences are dense throughout many of the areas in which construction would occur. Those residences adjacent to the construction footprint and haul routes would experience noise levels of 55 dB Leq or greater.

Individual sensitive receptors would be exposed to construction noise for several weeks to a full construction season, depending on the extent to which construction activities are staggered. Since short term, construction-related noise levels for Alternative 7a would exceed the applicable daytime standards of San Joaquin County (50 dBA Leq during daytime for outdoor activity areas), City of Stockton (55 dBA Leq during daytime for outdoor activity areas) and City of Manteca (50 dBA Leq during daytime for outdoor activity areas), impacts would be significant. The use of noise-reducing construction practices would reduce noise levels, but impacts would remain significant and unavoidable.

Vibration
Construction activities under Alternative 7a would potentially result in varying degrees of temporary groundborne vibration, depending on the operations and equipment used. Vibration spreads through the ground and vibration levels decrease with increasing distance from the source. Table 5-43 lists the typical construction equipment vibration levels at a distance of 25 feet and the distance at which the vibration levels would be attenuated to 80 VdB or less.

Table 5-43: Typical Construction Equipment Vibration
Equipment PPV Lv at 25 ft Ft to 80 VdB contour
Pile Driver (Impact) Upper Range 1.518 112 625
Typical 0.644 104 350
Pile Driver (vibratory) Upper Range 0.734 105 375
Typical 0.17 93 150
Large Bulldozer 0.089 87 90
Loaded trucks 0.076 86 85
Jackhammer 0.035 79 50
Construction of the closure structure at Smith Canal would require pile drivers. Whether vibratory pile drivers or impact pile drivers are used, the vibrations would not typically exceed the FTA standard (80 VdB for residential land uses) for any nearby sensitive receptors. However, the upper range for pile drivers could infrequently affect residences (i.e., sensitive receptors) which are within 625 feet of the closure structure construction. Because construction activities would be conducted only during the day time and because the vibration events in the upper range would likely occur infrequently, groundborne vibration from sheetpiling is unlikely to cause annoyance.

Equipment required for conventional and deep soil mixing cutoff wall construction would include truckmounted augers, excavators, backhoes, bulldozers, scrapers, rollers, graders, loaders, compactors and various trucks. Ground vibration would also be generated by haul trucks on area haul routes. The most intense generation of ground vibration would be associated with large bulldozers, which generate levels of 87 VdB at a distance of 25 feet. These levels would attenuate to 80 VdB at a distance of 90 feet. Vibrationsensitive receptors (i.e., residences) are located adjacent to haul routes and adjacent to the levee within 90 feet of the maximum construction limit areas. Vibration could exceed the FTA standard (80 VdB) for human annoyance at these receptors, although no nighttime hauling or construction activities would occur and sleep would not be disturbed. For Alternative 7a, the vibration impacts associated with levee construction and material hauling would thus be significant. The use of vibration-reducing construction practices would reduce vibration levels impacts would remain significant and unavoidable.

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San Joaquin County, CA Affected Environment and Environmental Consequences ALTERNATIVE 7B
Alternative 7b would include the same improvements in North and Central Stockton as Alternative 7a, but would also include repairs in RD 17. The overall project length (43.2 miles) would likely affect additional noise-and vibration-sensitive receptors in RD 17, primarily in Weston Ranch, Lathrop and Manteca.

Alternative 7b would include construction activities associated with cutoff walls, seepage berms and levee widening and raises in RD 17. These would involve recurring construction activities along the entire length of the site until construction completion. On-site equipment for construction activities would include excavators, backhoes, bulldozers, scrapers, rollers, graders, loaders, compactors and trucks.

Temporary noise levels at sensitive receptors would exceed the applicable daytime standards of San Joaquin County (50 dBA Leq during daytime for outdoor activity areas) and City of Stockton (55 dBA Leq during daytime for outdoor activity areas), construction-related noise impacts would be significant. These shortterm noise levels would result in increased annoyance and/or disrupted sleep for residential occupants and other sensitive receptors resulting in significant impacts. The use of noise-reducing construction practices would reduce noise levels but impacts would remain significant and unavoidable.

Vibration under Alternative 7b would affect sensitive receptors within 90 feet of project haul routes and construction boundaries and would infrequently affect the 2 sensitive receptors within 625 feet of the sheetpiling activities at Smith Canal. Vibration could exceed the FTA standard (80 VdB) for human annoyance at these receptors, although no nighttime hauling or construction activities would occur and sleep would not be disturbed. The vibration impacts associated with levee construction would result in significant impacts. The use of vibration-reducing construction practices would reduce impacts, but impacts would remain significant and unavoidable.

ALTERNATIVE 8A
Alternative 8a would include the same improvements in North and Central Stockton as Alternative 7a, but would include additional repairs along portions of Lower Calaveras River and along the Stockton Diverting Canal. Since the overall project length (34.1 miles) would be larger than Alternative 7a and smaller than Alternative 7b, Alternative 8a would likely affect more noise- sensitive and vibration-sensitive receptors than Alternative 7a and fewer than Alternative 7b.

Under Alternative 8a, temporary noise levels at noise sensitive receptors could exceed the applicable daytime standards of San Joaquin County (50 dBA Leq during daytime for outdoor activity areas) and City of Stockton (55 dBA Leq during daytime for outdoor activity areas), construction-related noise impacts would be significant. These short term noise levels would result in increased annoyance and/or disrupted sleep for occupants of residential dwellings and other sensitive receptors. The use of noise-reducing construction practices would reduce noise levels but impacts would remain significant and unavoidable.

Vibration under Alternative 8a would affect sensitive receptors within 90 feet of project haul routes and construction boundaries and would infrequently affect the sensitive receptors within 625 feet of the sheetpiling activities at Smith Canal. Vibration could exceed the FTA standard (80 VdB) for human annoyance at these receptors, although no nighttime hauling or construction activities would occur and sleep would not be disturbed. The vibration impacts associated with levee construction would thus be significant. The use of vibration-reducing construction practices would reduce levels of vibration, but impacts would remain significant and unavoidable.

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Construction of levee improvements under Alternative 8b would generate temporary, short-term and intermittent noise and vibration at or near individual noise-sensitive and vibration-sensitive locations along

53.7 miles of project reaches. Alternative 8b would include the same improvements in North and Central Stockton as Alternative 7a, except that it would include additional repairs along portions of Lower Calaveras River and along the Stockton Diverting Canal. Alternative 8b includes the same levee improvements in RD 17 as those described for Alternative 7b.

The noise and vibration impacts described for Alternative 8b are the same as those described for Alternative 7b except that additional sensitive receptors would be affected along portions of Calaveras River and the Stockton Diverting Canal. For the same reasons described for Alternative 7b, noise impacts and vibration impacts associated with levee and gate construction would be significant. The use of noise and vibration reducing construction practices would reduce noise and vibration levels, but impacts would remain significant and unavoidable.

Since short-term noise levels for Alternative 8b would exceed the applicable daytime standards of San Joaquin County (50 dBA Leq for outdoor activity areas), City of Stockton (55 dBA Leq for outdoor activity areas) and City of Manteca (50 dBA Leq for outdoor activity areas), construction-related noise impacts would be significant. The use of noise-reducing construction practices would reduce noise levels, but impacts would remain significant and unavoidable.

ALTERNATIVE 9A
Construction of levee improvements under Alternative 9a would generate temporary, short-term and intermittent noise and vibration at or near individual noise- and vibration-sensitive locations along 23.6 miles of project reaches.

Alternative 9a levee improvements and gates would be the same as those proposed under Alternative 7a, except that Alternative 9a would include construction of a flood bypass in Old Mormon Slough.

Noise and vibration impacts would be the same as Alternative 7a except that there would be potential to affect additional noise- and vibration-sensitive receptors along both sides of Old Mormon Slough.

The noise and vibration impacts described for Alternative 9a are the same as Alternative 7a except that additional sensitive receptors would be affected along Old Mormon Slough. For the same reasons as Alternative 7a, noise and vibration impacts associated with levee and gate construction would be significant. The use of noise- and vibration-reducing construction practices would reduce noise and vibration levels, but impacts would remain significant and unavoidable.

ALTERNATIVE 9B
Construction of levee improvements under Alternative 9b would generate temporary, short-term and intermittent noise and vibration at or near individual noise- and vibration-sensitive locations along 43.2 miles of project reaches.

Levee improvements and gates proposed in Alternative 9b would be the same as Alternative 7b, except that Alternative 9b would include construction of a flood bypass in Old Mormon Slough. So, noise and vibration impacts would be the same as Alternative 7a except that there would be a potential to affect additional noise- and vibration-sensitive receptors along both sides of Old Mormon Slough.

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San Joaquin County, CA Affected Environment and Environmental Consequences For the same reasons as Alternative 7a, noise and vibration impacts from levee and gate construction would be potentially significant. The use of noise- and vibration-reducing construction practices would reduce noise and vibration levels, but impacts would remain significant and unavoidable.

As described for Alternative7b, vibration under Alternative 9b would affect sensitive receptors within 90 feet of project haul routes and construction boundaries and would infrequently affect the sensitive receptors within 625 feet of the sheetpiling activities at Smith Canal. Vibration could exceed the FTA standard (80 VdB) for human annoyance at these receptors. No nighttime hauling or construction activities would occur, but daytime sleep could be disturbed. The vibration impacts associated with levee construction would thus be significant. The use of vibration-reducing construction practices would reduce vibration levels, but impacts but would remain significant and unavoidable.

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MITIGATION
Implementing the following mitigation measures would reduce the impact, but may not reduce noise and vibration levels at all times to a less than significant level because of the close proximity of noise-sensitive receptors to construction activities. These sensitive receptors are located along the North and Central Stockton reaches of all of the alternatives and additionally along Westin Ranch, Lathrop and Manteca in RD 17 for all of the “b” alternatives. In addition, predicted noise levels may not meet the applicable standards for local exterior noise for residential land uses and because of the limited feasibility of mitigating construction noise to acceptable levels. Therefore, these short-term impacts would be significant and unavoidable for all of the action alternatives (Alternatives 7a, 7b, 8a, 8b, 9a and 9b).  The contractor shall prepare a construction noise and vibration plan prior to construction.  The contractor shall employ vibration-reducing construction practices.  The contractor shall employ noise-reducing construction practices.  All construction equipment shall be equipped with noise-reduction devices such as mufflers to minimize construction noise and all internal combustion engines shall be equipped with exhaust and intake silencers in accordance with manufacturers’ specifications.  Equipment that is quieter than standard shall be used, including electrically powered equipment instead of internal combustion equipment, where use of such equipment is a readily available substitute that accomplishes project tasks in the same manner as internal combustion equipment.  The use of bells, whistles, alarms and horns shall be restricted to safety warning purposes only.  Noise-reducing enclosures shall be used around stationary noise-generating equipment (e.g., compressors and generators at slurry pond locations).
 Mobile and fixed construction equipment (e.g., compressors and generators), construction staging and stockpiling areas and construction vehicle routes shall be located at the most distant point feasible from noise-sensitive receptors.
 When noise-sensitive uses subject to prolonged construction noise and are located within 740 feet of construction in Stockton, Lathrop or unincorporated areas of San Joaquin county or within 1140 feet of construction in Manteca, noise attenuating buffers such as structures, truck trailers or soil piles shall be located between noise generation sources and sensitive receptors.  Before construction activity begins within 740 feet of one or more residences or businesses (or within 1140 feet of residences or businesses in Manteca), the local sponsors (SJAFCA) shall provide written notification to the potentially affected residents or business owners, identifying the type, duration and frequency of construction activities. A noise disturbance coordinator shall be designated and contact information shall be provided in the notices and posted near the project area in a conspicuous location that it is clearly visible to nearby receptors most likely to be disturbed. The coordinator shall manage complaints and concerns resulting from noise-generating activities. The severity of the noise concern would be assessed by the coordinator and if necessary, evaluated by a qualified noise control engineer.  The project proponent (USACE, CVFPB and/or SJAFCA) shall ensure that all heavy trucks are properly maintained and equipped with noise control (e.g., muffler) devices in accordance with manufacturers’ specifications at each work site during project construction to minimize construction traffic noise effects on sensitive receptors.
 Before haul truck trips are initiated during construction season on roads within 90 feet of residences located along haul routes, written notification shall be provided to potentially affected residents identifying the hours and frequency of haul truck trips. Notifications provide contact information for a noise disturbance coordinator identified above and also identify a mechanism for residents to register complaints with the appropriate jurisdiction if haul truck noise levels are overly intrusive or occur outside the exempt daytime hours for the applicable jurisdiction.

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PUBLIC HEALTH AND ENVIRONMENTAL HAZARDS
This section describes the affected environment and environmental consequences relating to hazardous, toxic and radiological materials and waste for the LSJR project. For the purposed of this section, the term “hazardous materials” refers to both hazardous substances and hazardous wastes. A hazardous material is defined as “a substance or material that is capable of posing an unreasonable risk to health, safety and property when transported in commerce” (49 CFR Section 171.8). California Health and Safety Code Section 25501 defines a hazardous material as follows:
“Hazardous material” means any material that, because of its quantity, concentration or physical or chemical characteristics, poses a significant present or potential hazard to human health and safety or to the environment if released into the workplace or the environment. “Hazardous materials” include, but are not limited to, hazardous substances, hazardous waste and any material which a handler or the administering agency has a reasonable basis for believing that it would be injurious to the health and safety of persons or harmful to the environment if released into the workplace or the environment.

Hazardous wastes are defined in California Health and Safety Code Section 25141(b) as wastes that:
…because of their quantity, concentration or physical, chemical or infectious characteristics, [may either] cause or significantly contribute to an increase in mortality or an increase in serious illness[ or] pose a substantial present or potential hazard to human health or the environment when improperly treated, stored, transported, disposed of or otherwise managed.

ENVIRONMENTAL SETTING
Regulatory Framework
The principal Federal regulatory agency responsible for the safe use and handling of hazardous materials is the EPA. Key Federal statutes pertaining to hazardous wastes are listed below. Other applicable Federal regulations are contained primarily in CFR Titles 29, 40 and 49.

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 Comprehensive Environmental Response, Compensation and Liability Act, 42 U.S.C. §9601, et seq.
 Hazardous Materials Regulations (Title 49 CFR, Parts 100-185) (rail transport)  Resource Conservation and Recovery Act, 42 U.S.C. §6901, et seq.  Worker Safety Requirements
State
 Asbestos Airborne Toxic Control Measure for Construction, Grading, Quarrying and Surface Mining Operations
 California Emergency Response Plan (Governor’s Office of Emergency Services)  Emergency Services Act
 Hazardous Materials Release Response Plans and Inventory Act of 1985  Hazardous Waste Control Act
 Health and Safety Code, Division 20, Chapter 6.95, Article 1)  Worker Safety Requirements (Title 8 California Code of Regulations (CCR)) Local
 City of Lathrop General Plan (2004) (Goal 4, Policies 4 and 6)  City of Manteca General Plan (2003) (Goal S-5, Policies S-P-15, S-P-16, S-P-17; Goal S-6)  City of Stockton General Plan (2007)
 San Joaquin County General Plan (Policies 1, 2 and 4) Existing Conditions
A Hazardous, Toxic and Radioactive Waste (HTRW) Summary Report (USACE, 2014) was completed for all areas where construction work could occur under any of the action alternatives. A Phase I Environmental Site Assessment of Old Mormon Slough was also completed (Kleinfelder, 2013). The assessment consisted of a records investigation, interviews and site reconnaissance and focused on the Old Mormon Slough between the Stockton Diverting Canal and the Stockton Deep Water Ship Channel. The HTRW Summary Report consisted of a records and literature review focused on the construction footprint and the area immediately adjacent for all of the LSJR action alternatives. The area of HTRW study for this summary report was defined as buffer areas within 0.25 miles along 40 miles of the proposed levees identified in Alternatives 7a, 7b, 8a, 8b, 9a and 9b excluding the Old Mormon Slough (see Chapter 3, Figures 3-12 and 3-13 [Alternatives 9a and 9b] for the location of Mormon Slough). The levees are located near the city of Stockton, San Joaquin County, California.

There are 40 Underground Storage Tank (UST) sites in northeast and northwest Stockton sections and 20 known Leaking Underground Storage Tanks (LUST) in both sections. The EPA’s Emergency Response Notification System (ERNS) records show incidents of releases of oil and hazardous substances. There are a large number of such incidents throughout the HTRW area of study, especially in northeast and northwest Stockton. Several of the sites referred to the Regional Water Quality Control Board are likely to contain contaminated groundwater on-site and potentially off-site. These groundwater HTRW sites could affect worker safety, dewatering operations or excavation work depending on the depth to groundwater and magnitude of the groundwater plumes. Out of the 61 sites in the HTRW study area listed in the GeoTracker ATTACHMENT D 1387
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San Joaquin County, CA Affected Environment and Environmental Consequences website, 36 are in the “Completed – Case Closed” status and the majority of those open sites are undergoing remediation or being assessed by California Water Board.

Overall, the EnviroStor website showed a total of 22 hazardous waste and clean-up sites in the HTRW study area. These sites are present in all of the alternatives. The sites were primarily chemical companies and petroleum companies all located in northeast and northwest Stockton. Out of the 22 sites, 8 of them were in “No Further Action” status and the rest were either open or referred to other agencies. In addition to the hazardous materials described above, buildings and other infrastructure in the project area may include component materials that are hazardous, such as lead paint or asbestos.

ASSESSMENT METHODS AND BASIS OF SIGNIFICANCE
Assessment Methods
Regulatory database search reports and regulatory agencies’ websites were reviewed and assessed for HTRW sites in the study area. For the purposes of the HTRW analysis, the study area was defined as buffered areas within 0.25 miles along 40 miles of the proposed levees identified in Alternatives 7a, 7b, 8a, 8b, 9a and 9b that are located in northeast, northwest and south Stockton.

In order to identify HTRW sites in the study area, USACE:
 Reviewed Federal, State and local environmental databases;  Reviewed hazardous waste sites and clean-up sites in EnviroStor of California (CA) Department of Toxic Substances Control (DTSC) and GeoTracker of CA State Water Resources Control Board and;
 Reviewed information about Naturally Occurring Asbestos in the CA Department of Conservation website.

The following sources were reviewed for HTRW sites in the HTRW Study Area (Fig 2).  Environmental Data Resources (EDR) Database Search Reports (in Attachments 1-6)  EnviroStor website (http://www.envirostor.dtsc.ca.gov/public)  GeoTracker web site (http://geotracker.waterboards.ca.gov)  Department of Conservation
(http://www.conservation.ca.gov/cgs/minerals/hazardous_minerals/asbestos/Pages/index.aspx) ATTACHMENT D 1388
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San Joaquin County, CA Affected Environment and Environmental Consequences Basis of Significance
The thresholds for determining the significance of impacts for this analysis are based on the environmental checklist in Appendix G of the State CEQA Guidelines. These thresholds also encompass the factors taken into account under NEPA to determine the significance of an action in terms of its context and the intensity of its impacts. The alternatives under consideration were determined to result in a significant impact related to hazards and hazardous materials if they would do any of the following:
 Create a significant hazard to the public or the environment through the routine transport use or disposal of hazardous materials or through reasonably foreseeable upset and accident conditions involving the release of hazardous materials into the environment.  Emit hazardous emissions or involve the handling of hazardous or acutely hazardous materials, substances or waste within one-quarter mile of an existing or proposed school.  Be located on a site that is included on a list of hazardous materials sites compiled pursuant to California Government Code Section 65962.5 and, as a result, create a significant hazard to the public or the environment (Health & Safety Code § 65962.5).

ALTERNATIVE 1 - NO ACTION
Under the No Action Alternative, the levee improvement project would not be constructed, therefore, there would be no construction-related effects from HTRW (e.g. accidental spills of hazardous materials) in the project area. However, the existing flood risk would continue, which could potentially lead to significant flooding and levee failures in a future flood event.

Without levee improvements, there is the continued high risk of levee failure and continuing under seepage and loss of levee foundation soils. If a levee overtopping or breach were to occur, flood fighting and other emergency response activities would occur. Flood waters could release contaminants from buildings and other infrastructure (e.g., lead paint and asbestos), stored chemicals, septic systems and flooded vehicles, all of which could contaminate the SJR, the Calaveras River, French Camp Slough and Delta sloughs, as well as soil and groundwater in the project area. These contaminants would likely exceed acceptable established water quality standards and impair beneficial uses of the river, its tributaries and sloughs in project area, including downstream drinking water intakes. Effects on the water supply system could be particularly severe in a flood event, as a single break in a water delivery pipe or main could contaminate the entire city’s water supply. All breaks and leaks would need to be repaired and the pipes of every house would need to be flushed to remove contamination before residents and businesses could rely on safe water.

Depending on the severity and location of the flooding and contamination, this effort could take a significant amount of time.

Flood damage to homes and other structures can render them dangerous due to structural damage and contamination. Electrical systems could be damaged by flooding, posing potential fires and natural gas leaks that could result in poisoning through inhalation of fumes or could cause a sudden explosion if sparked. The likelihood of a significant amount of mold production is high after a flood event. Mold not only threatens the physical integrity of structures, but also poses its own health risks. Mold can cause lung infections, skin irritations and other health dangers, especially for those with asthma, allergies or suppressed immune systems. Additionally, the floodwaters themselves and ponds left behind, could provide a wide breeding ground for mosquitoes and the incidence of West Nile Virus and other diseases would likely increase. The magnitude of the impacts described above would depend upon the location of the levee breach, severity of the storm and river flows at the time of flooding. Predicting these events and providing a determination of significance is not possible based on available information. Thus, identification of potential effects from levee failure is too speculative for meaningful consideration.

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San Joaquin County, CA Affected Environment and Environmental Consequences Under the No Action Alternative, regular O&M of the levee system would continue as presently executed by the local maintaining entities (subject to revision of the governing O&M manual). Such activities include hand and mechanical (mower) removal of weeds, spraying of weeds with approved pesticides, minimal tree or shrub trimming up to four times a year, monthly control of burrowing rodent activity by baiting with pesticide and reconditioning of levee slope and road as needed. Normal O&M activities would be shortterm and small scale; thus, impacts from HTRW from continued O&M activities would be less than significant.

ALTERNATIVE 7A
Construction activities for Alternative 7a would involve the use of hazardous materials such as fuels and lubricants to operate construction equipment and vehicles such as excavators, compactors, haul trucks and loaders. In some parts of the project area, these materials would be used or transported within one quarter mile of an existing school. Construction contractors would be required to use, store and transport hazardous materials in compliance with Federal, State and local regulations during project construction and operation.

However, fuels and lubricants could be accidentally released into the environment at the construction site and along haul routes, causing environmental or human exposure to these hazards.

The implementation of environmental commitments, including SWPPP, BSSCP, SPCCP and the implementation of avoidance, minimization and mitigation measures, would ensure minimal risk of accidental spills and releases into the environment. Any hazardous substance encountered during construction would be removed and properly disposed of by a licensed contractor in accordance with Federal, State and local regulations. Compliance with applicable regulations would reduce the potential for accidental release of hazardous materials during transport and construction activities.

There is the potential that known or previously undocumented hazardous materials could be encountered at project sites. Where buildings or other infrastructure must be moved or removed, there would be a potential for exposure to hazards, such as lead paint and asbestos. Excavation and construction activities at or near areas of currently unrecorded soil or groundwater contamination could result in the exposure of construction workers, the general public and the environment to hazardous materials such as petroleum hydrocarbons, pesticides, herbicides, fertilizers, contaminated debris or elevated levels of other chemicals that could be hazardous. There are known sites within the project area that contain hazardous materials. All known HTRW sites are required to be remediated in accordance with Federal, State and local laws by the nonFederal sponsor prior to project construction. No construction activities would occur in proximity to these sites until they have been completely remediated and meet all regulatory requirements. Construction activities in the vicinity of known or potentially unknown, recognized environmental concerns could result in public health hazards if they are not properly addressed prior to construction.

Implementation of Alternative 7a would result in post-construction O&M activities conducted per the approved USACE O&M manual applicable to this reach. Such activities include hand and mechanical (mower) removal of weeds, spraying of weeds with approved pesticides, minimal tree or shrub trimming up to four times a year, monthly control of burrowing rodent activity by baiting with pesticide and reconditioning of levee slope and road with a bull dozer as needed. Normal O&M activities would be shortterm and small scale; therefore, impacts to HTRW would be less than significant.

The risk of incidental release of hazardous materials during their transport and use in project construction activities is low. Because normal O&M activities would be short-term and small scale and with implementation of avoidance, minimization and mitigation measures, impacts from construction activities in the vicinity of known or potentially unknown recognized environmental concerns would reduce impacts to less than significant.

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San Joaquin County, CA Affected Environment and Environmental Consequences ALTERNATIVE 7B
Alternative 7b includes all of the same sites as Alternative 7a, but differs because it also includes RD 17.

Alternative 7b construction activities would involve the use of hazardous materials such as fuels and lubricants to operate construction equipment and vehicles. In some parts of the project area, these materials would be used or transported within 0.25 mile of an existing school. These potential impacts and regulation requirements are described under Alternative 7a. Compliance with applicable regulations would reduce the potential for accidental release of hazardous materials during transport and construction.

The risk of incidental release of hazardous materials during their transport and use in project construction activities is low and because normal O&M activities would be short term and small scale and with the implementation of avoidance, minimization and mitigation measures, impacts from construction activities in the vicinity of known or potentially unknown recognized environmental concerns would reduce impacts to less than significant levels.

ALTERNATIVE 8A
Alternative 8a includes all of the same sites as Alternative 7a, but differs in Central Stockton where additional levee improvements are proposed on the Lower Calaveras River and the Stockton Diverting Canal. Construction activities for Alternative 8a would involve the use of hazardous materials such as fuels and lubricants to operate construction equipment and vehicles. In some parts of the project area, these materials would be used or transported within 0.25 mile of an existing school. These potential impacts are described under Alternative 7a. Compliance with applicable regulations would reduce the potential for accidental release of hazardous materials during transport and construction activities.

The risk of incidental release of hazardous materials during their transport and use in project construction activities is low and because normal O&M activities would be short-term and small scale and with the implementation of avoidance, minimization and mitigation measures, impacts from construction in the vicinity of known or potentially unknown recognized environmental concerns would reduce impacts to less than significant levels.

ALTERNATIVE 8B
Alternative 8b includes all of the same sites as Alternative 7b, but differs in Central Stockton where additional levee improvements are proposed on the Lower Calaveras River and the Stockton Diverting Canal. Construction activities for Alternative 8b would involve the use of hazardous materials such as fuels and lubricants to operate construction equipment and vehicles. In some parts of the project area, these materials would be used or transported within 0.25 mile of an existing school. These potential impacts are described under Alternative 7a. Compliance with applicable regulations would reduce the potential for accidental release of hazardous materials during transport and construction.

ALTERNATIVE 9A
Alternative 9a includes the same sites as Alternative 7a, but differs in the addition of a flood bypass that would divert floodflows from the Stockton Diverting Canal into and through the Mormon Channel Bypass.

Construction activities would involve the use of hazardous materials such as fuels and lubricants to operate ATTACHMENT D 1391
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San Joaquin County, CA Affected Environment and Environmental Consequences construction equipment and vehicles. In some parts of the project area, these materials would be used or transported within 0.25 mile of an existing school. These potential impacts are described under Alternative 7a. Compliance with applicable regulations would reduce the potential for accidental release of hazardous materials during transport and construction activities.

ALTERNATIVE 9B
Alternative 9b includes the same sites as Alternative 7b, but differs in the addition of a flood bypass that would divert floodflows from the Stockton Diverting Canal into and through the Mormon Channel Bypass.

Construction activities would involve the use of hazardous materials such as fuels and lubricants to operate construction equipment and vehicles. In some parts of the project area, these materials would be used or transported within 0.25 mile of an existing school. These potential impacts are described under Alternative 7a. Compliance with applicable regulations would reduce the potential for accidental release of hazardous materials during transport and construction activities.

The risk of incidental release of hazardous materials during their transport and use in construction is low and because normal O&M activities would be short-term and small scale and with the implementation of avoidance, minimization and mitigation measures, impacts from construction activities in the vicinity of known or potentially unknown recognized environmental concerns would reduce impacts to less than significant levels.

MITIGATION
Each of the action alternatives involve the transport and use of hazardous materials. These are materials commonly used in construction of levees and associated infrastructure. Parts of each action alternative are within 0.25 mile of 1 or more schools. The project partners and their construction contractor would work with local schools prior to beginning construction to ensure that all appropriate measures are in place to reduce risk to schools, students, teachers and other employees and maintain less than significant impacts from hazardous emissions and transport and use of hazardous materials.

Alternatives 7a, 7b, 8a, 8b, 9a and 9b all occur on or in close proximity to, hazardous material sites, possessing the potential to cause hazards to construction workers and the public. These alternatives all include the potential for encountering hazardous materials, such as lead paint and asbestos) during removal or relocation of buildings and other infrastructure. Project areas would be tested for contaminants prior to construction and any materials found would be disposed of in accordance with all Federal, State and local regulations at an approved disposal site. Implementation of these mitigation measures would reduce the impacts from hazardous materials at project sites to less than significant.

If significant time has elapsed between approval of this document and construction, additional investigations should be done to reduce risk. If construction activities would occur in close proximity to sites identified in the existing conditions section or in the Phase I Site Assessment, a Phase II Environmental Site Assessment should also be conducted. This would further reduce the risk of exposure to workers and the public during construction and assist in the remediation planning. If necessary, the assessment would include an analysis of soil or groundwater samples for the potential contamination sites that have not yet been covered by previous investigations before construction activities begin.

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San Joaquin County, CA Affected Environment and Environmental Consequences Recommendations in Phase I and Phase II Environmental Site Assessments to address any contamination that is found would be implemented before initiating ground-disturbing activities. In addition, the following measures would be implemented before ground-disturbing or demolition activities begin, in order to reduce health hazards associated with potential exposure to hazardous substances:
 Complete a Phase I Site Assessment prior to completing preconstruction designs and initiating construction.
 Prepare a site plan that identifies any necessary remediation activities appropriate for proposed land uses, including excavation and removal of contaminated soils and redistribution of clean fill material on the project site. The plan would include measures that ensure the safe transport, use and disposal of contaminated soil and building debris removed from the site, as well as any other hazardous materials. In the event that contaminated groundwater is encountered during site excavation activities, the contractor would report the contamination to the appropriate regulatory agencies, dewater the excavated area and treat the contaminated groundwater to remove contaminants before discharge into the sanitary sewer system. The contractor would be required to comply with the plan and applicable Federal, State and local laws.  Notify appropriate Federal, State and local agencies if evidence of previously undiscovered soil or groundwater contamination is encountered during construction. Any contaminated areas would be cleaned up in accordance with the recommendations of the Central Valley RWQCB, California DTSC or other appropriate Federal, State or local regulatory agencies.  A worker health and safety plan would be prepared before the start of construction that identifies, at a minimum, all contaminants that could be encountered during construction; all appropriate worker, public health and environmental protection equipment and procedures to be used during project activities; emergency response procedures; the most direct route to the nearest hospitals; and a Site Safety Officer. The plan would describe actions to be taken if hazardous materials are encountered on-site, including protocols for handling hazardous materials, preventing their spread and emergency procedures to be taken in the event of a spill.  Retain licensed contractors to remove all underground storage tanks.

CULTURAL RESOURCES
This chapter describes the environmental setting associated with cultural resources, assesses the effects to cultural resources that would result from implementation of the proposed action and presents mitigation measures that would reduce these effects to less than significant. The key sources of data and information used in the preparation of this chapter are listed below.  Review of existing information.
 Consultation with interested parties.
 Archival research.
 Reconnaissance surveys of selected previously recorded cultural resources.

Cultural resources are defined in this chapter as prehistoric and historic archaeological sites, the historic built environment and traditional cultural properties.

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ENVIRONMENTAL SETTING
Regulatory Framework
Federal
National Historic Preservation Act
The proposed project would require that USACE comply with Section 106 of the National Historic Preservation Act of 1966, as amended (NHPA) and its implementing regulations (36 CFR 800, Section 106). Section 106 requires that, before beginning any undertaking, a Federal agency must take into account the effects of the undertaking on historic properties (cultural resources listed or eligible for listing on the National Register of Historic Places [NRHP]) and afford the Advisory Council on Historic Preservation an opportunity to comment on these actions. Federal agencies may comply with Section 106 by either completing the management steps indicated in the regulations (36 CFR Part 800) or preparing an agreement document that describes the particular process an agency will use to complete the same steps for a specific set of undertakings.

Cultural resources are eligible for the NRHP if they have integrity and significance as defined in the regulations for the NRHP. Four primary criteria define significance; a property may be significant if it displays 1 or more of the characteristics (36 CFR 60.4). (Criterion A) It is associated with events that made a significant contribution to the broad patterns of our history; (Criterion B) is associated with the lives of people significant in our past; (Criterion C) embodies the distinct characteristics of a type, period or method of construction or that represents the work of a master or that possesses high artistic values or represents a significant and distinguishable entity whose components may lack individual distinction; or (Criterion D) it has yielded or is likely to yield, information important in prehistory or history.

Some types of cultural resources are not typically eligible for the NRHP. These resources consist of cemeteries, birthplaces, graves of historical figures, properties owned by religious institutions or used for religious purposes, structures that have been moved from their original locations, reconstructed historic buildings, properties primarily commemorative in nature and properties that have achieved significance within the past 50 years. These property types may be eligible for the NRHP, however, if they are integral parts of eligible districts of resources or meet the criteria considerations described in 36 CFR 60.4.

In addition to possessing significance, a property must also have integrity to be eligible for listing in the NRHP. The principle of integrity has seven aspects: location, design, setting, materials, workmanship, feeling and association (36 CFR 60.4). To retain historic integrity, a property needs to possess several and usually most, of these aspects (National Park Service, 2002). The evaluation of a resource’s integrity in relation to its significance will be conducted as prescribed in National Register Bulletin No. 15: How to Apply the National Register Criteria for Evaluation (National Park Service, 2002).

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San Joaquin County, CA Affected Environment and Environmental Consequences The Section 106 review process typically consists of the following major steps:
 Identify the Federal agency undertaking.
 Identify the area of potential effects.
 Initiate Section 106 process.
 Identify historic properties.
 Evaluate effects to historic properties.
 Resolve adverse effects.

State
Under CEQA, a cultural resource is considered important if it meets the definition of “historical resource or unique archaeological resource.” Public Resource Code (PRC) Section 5020.1(j)) states:
“Historical resource” includes, but is not limited to, any object, building, structure, site, area, place, record or manuscript which is historically or archaeologically significant or is significant in the architectural, engineering, scientific, economic, agricultural, educational, social, political, military or cultural annals of California. Historical resources may be designated as such through 3 different processes.

Official designation or recognition by a local government pursuant to local ordinance or resolution (PRC Section 5020.1(k)). A local survey conducted pursuant to PRC Section 5024.1(g). Listed in or eligible for listing in the NRHP (PRC Section 5024.1(d)(1). The process for identifying historical resources typically is accomplished by applying the criteria for listing in the CRHR (14 CCR 4852), which states that a historical resource must be significant at the local, state or national level under one or more of the four criteria. (Criterion 1) It is associated with events that have made a significant contribution to the broad patterns of California’s history and cultural heritage. (Criterion 2) It is associated with the lives of persons important in our past. (Criterion 3) It embodies the distinctive characteristics of a type, period, region or method of construction or represents the work of a master or possesses high artistic values. (Criterion 4) It has yielded or may be likely to yield, information important in prehistory or history.

To be considered an “historical resource” for the purpose of CEQA, the resource must also have integrity, which is the authenticity of a resource’s physical identity evidenced by the survival of characteristics that existed during the resource’s period of significance. Resources, therefore, must retain enough of their historic character or appearance to be recognizable as historical resources and to convey the reasons for their significance. Integrity is evaluated with regard to the retention of location, design, setting, materials, workmanship, feeling and association. It also must be judged with reference to the particular criteria under which a resource is eligible for listing in the CRHR (14 CCR 4852[c]).

The State also recognizes the importance of “unique archaeological resources” defined in PRC Section 21083.2 as an archaeological artifact, object or site about which it can be clearly demonstrated that, without merely adding to the current body of knowledge, there is a high probability that it meets any of the following criteria.
 Contains information needed to answer important scientific research questions and for which there is a demonstrable public interest.
 Has a special and particular quality such as being the oldest of its type or the best available example of its type.
 Is directly associated with a scientifically recognized important prehistoric or historic event or person.

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San Joaquin County, CA Affected Environment and Environmental Consequences In most situations, resources that meet the definition of a unique archaeological resource also meet the definition of historical resource. As a result, it is current professional practice to evaluate cultural resources on their eligibility for listing in the CRHR. For the purposes of this cultural resources study, a resource is considered important if it meets the CRHR eligibility (significance and integrity) criteria.

Existing Conditions
Cultural History
This section provides an overview of the context and chronology of the human use of the LSJR Basin and the Stockton region. Portions of this section were excerpted from Rosenthal and Whittaker (2009), AECOM (2010) and Jones, Bartoy, Blind and Holson (2006).

Prehistoric Setting
The complexity of the archaeological record in the central California Delta region has resulted in the development and refinement of local sequences with specific cultural traits and chronologies (Hughes, 1994). Fredrickson (1974) proposed a tripartite scheme - Archaic, Emergent and Ethnographic - each with subdivisions, appropriate characteristics and chronological ranges. The Lower Archaic (10,000-6000 B.P.) and the Initial Middle Archaic (6000-4500 B.P.) are not well known from San Joaquin County and are primarily represented from the research completed at Los Vaqueros Reservoir to the southwest (Meyer and Rosenthal, 1997). The other divisions of the Archaic, Emergent and Ethnographic are reasonably well represented in the central Delta area. Additional details on the chronology and characteristics of these cultural divisions are presented in Fredrickson (1994a-b) and summarized below.

The Terminal Archaic period is noted as having side-notched and stemmed projectile points, rectangular abalone ornaments, shaped and unshaped mortars and pestles and rectangular Olivella shell beads (Fredrickson, 1966). Subsistence focused on nuts and berries as well as bay-shore resources (shellfish, marine fishes and mammals), freshwater fish, shellfish and terrestrial mammals (Banks and Orlins, 1985; Simons, 1992).

Upper Archaic sites are characterized by a bone tool and ornament industry and unshaped and well-shaped mortars and pestles. Subsistence was still centered on nuts and seeds and faunal assemblages indicate an inclusion of marine and/or mammal resources (Broughton, 1997; Fredrickson, 1968). The presence of ocean shellfish in the archaeological record indicates a growing reliance on marine resources in interior valley sites (Fredrickson, 1968).

The Meganos Culture began to appear in the San Joaquin Valley and Delta during the Upper Archaic. It spread quickly into Contra Costa County and other parts of the Bay Area (Bennyhoff, 1968; Bennyhoff and Hughes, 1987). The Meganos Culture has been characterized as a blend of bay and Delta populations.

The time period between 1300 B.P. and 1100 B.P. was one of social change and upheaval in the Delta and Central Valley. The southern Wintuan groups (ancestral Patwin) pushed the Meganos peoples into the Sacramento Delta and the Bay Miwok groups from the West Delta to Suisan Bay (Bennyhoff, 1994b).

Costanoan groups began to move across the Carquinez Strait. Meganos cemeteries in the Alameda and Diablo districts were abandoned during this turbulent 200 year period (see Bennyhoff, 1994a-c). After 900 B.P., the Meganos peoples integrated with the Valley Yokuts groups in the San Joaquin Valley (Bennyhoff, 1994c).

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San Joaquin County, CA Affected Environment and Environmental Consequences During the Emergent Period, cremations became quite common and the bow and arrow were introduced with the concomitant use of small projectile points (Moratto, 1984; Schenck and Dawson, 1929). Bedrock mortar milling stations appear early in the Emergent Period and were used in association with other portable milling equipment. Nuts, berries and seeds were collected and processed. Large terrestrial mammals (e.g., deer, elk) appear to have been favored. Marine shellfish and marine fishes appear inland in much larger quantities than in previous periods (Fredrickson, 1968). Emergent Period sites, typically identified as large mound villages, are found every few miles along the SJR and its major tributaries.

Ethnographic Setting
The Northern Valley Yokuts occupied the land on each side of the SJR from the Delta to south of Mendota when first encountered by the Spanish. The Yokuts’ occupation of the northern parts of the Diablo range may be relatively recent, as linguistic evidence points toward an earlier Miwok occupation. The late prehistoric Yokuts were probably the largest indigenous culture in pre-contact California.

European contact with the Northern Valley Yokuts began with intermittent trips by Spanish explorers traveling through the Sacramento–San Joaquin Valley in the late 1700s and early 1800s. Missionaries lured or captured many Yokuts and kept them in various missions, although many escaped and returned home to the valley. Skirmishes between Yokut raiding parties and the Spanish and other Euroamericans resulted from repeated cattle rustling, which ultimately lead to the deaths of numerous Yokut individuals. A malaria epidemic in 1833 greatly diminished the Native population by killing thousands of Yokuts and people of surrounding groups. The local population was further reduced by the rapid appearance of miners during the Gold Rush era. Despite the fact that there was no gold in the Yokuts’ territory, miners making their way to the gold fields caused upheaval. The remaining native populations were later displaced by miners, who returned to farm the area (Wallace, 1978).

Historic-Era Setting
Spanish missionaries were among the first recorded European visitors to the study area (Bakic and Lewiston, 1999). In 1776, Juan Batista de Anza, along with Friar Pedro Font, traveled south along a portion of the SJR with a party of immigrants from Monterey (Beck and Haase, 1974). Other eighteenth-century explorers of the area included Pedro Fages (1772) and Francisco Eliza (1793). Nearly 30 years later, Moraga completed more intensive explorations into the area, exploring some distance up and down the Mokelumne and Cosumnes rivers (Beck and Haase, 1974).

The establishment of the Spanish mission system ensured strong Hispanic influence throughout early California. Mexican influences remained even after the succession of Alta California to the U.S. in 1848 (Beck and Hasse, 1974). Hispanic relations with Native Americans were strained as demonstrated by the Stanislaus War fought in southern San Joaquin County beginning in 1828 (Keefe, 2004).

The first Euroamerican to traverse the area was probably Jedediah Strong Smith, who opened the Sacramento Trail in the late 1820s (Jones and Stokes, 2004). In 1832, French-Canadian hunters and an assemblage of travelers from Jedediah Smith’s party, Peter Ogden’s party and Ewing Young’s party first occupied the area known as French Camp, four miles south of present-day Stockton. The hunters were employed by the Hudson’s Bay Company to trap beaver, mink, bear and other fur-bearing animals.

Rancho del Campo de los Franceses, was established for the French-Canadian fur trappers of the Hudson’s Bay Company. Charles M. Weber, a native of Germany, traveled to French Camp on his way into California with the Bidwell-Bartleson party in the fall of 1841 (Hoover et al., 1990). Weber eventually settled in Pueblo de San José and went into partnership with William Gulnac, a blacksmith. In 1844, Gulnac received a large land grant, which included both French Camp and the site of the present-day Stockton. Gulnac and ATTACHMENT D 1397
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San Joaquin County, CA Affected Environment and Environmental Consequences Weber organized a company of 12 men for the purpose of forming a colony at French Camp, which was the first colony of white settlers to settle land in the San Joaquin Valley (Hoover et al., 1990).

The city of Stockton first started when Weber turned his strategy from gold mining, in late 1848, to supplying gold-seekers. To this end, he took over Gulnac’s portion of their joint Spanish land grant (Rancho del Campo de los Franceses) in 1849 (City of Stockton, 2011; Schlichtmann and Paden, 1986). The area currently known as Weber Point is the location of his first permanent residence in Stockton. Stockton was named by Weber in honor of Commodore Robert F. Stockton, although he later regretted it (Tinkham 1880).

Stockton was incorporated on July 23, 1850 by the County Court and the first city election was held on July 31, 1850 (City of Stockton, 2011). Stockton received its charter from the State of California in 1851. Early settlers of Stockton resembled those of other California settlements and included gold seekers from Asia, Africa, Australia, Europe, the Pacific Islands, Mexico and Canada (City of Stockton, 2011).

The Port of Stockton was the first and is still the largest, inland seaport in California. The first cargo boat traversed the San Joaquin in 1846. Two years later, in 1848, the first ferry service was established and the first freight vessel visited Stockton (Tinkham, 1880; Port of Stockton, 2014). During the 1850s, the port had become a center of commodity shipping and the supply center for the southern goldfields with 2000 to 3000 people landing in April of 1850 on the way to the gold fields (Schlichtmann and Paden, 1986; Tinkham, 1880). Supplies would be unloaded at Stockton and then either ported via stage, wagon and eventually train to the southern mines (Schlichtmann and Paden, 1986).

By the 1860s, gold production was declining while agriculture was increasing in the region. From 1890 to 1920, Stockton was a very active port city. Grain was the major cargo for the ocean vessels that visited the port (McElhiney, 1992). Due to the export of farming commodities, Stockton grew into a major commercial center. By the late 1880s, it was a highly industrialized California city, second only to San Francisco (McElhiney, 1992). The Stockton Deep Water Ship Channel was completed and the Port of Stockton was modernized in 1933. Across the river from the Port of Stockton is Rough and Ready Island, which was developed into a U.S. Naval Supply Base during World War II and was important in the development of modern supply and transport methods. Shipping remains important to Stockton today.

The City of Stockton sits along the southeastern edge of the Delta and important historical themes from the Delta are mirrored in the development of the Stockton Area including agriculture, irrigation and reclamation. Early farming consisted primarily of subsistence gardening during and following the Gold Rush, but the growth of the agricultural industry in the Delta was steady and by late 1870s, market gardens near Stockton were developing into formidable competitors for the San Francisco produce trade, which was dominated by Santa Clara Valley and bay area locations. By 1883, large amounts of garden vegetables were being shipped to San Francisco after the daily harvest was picked up by river steam ships. Thompson (1957) noted that the transition of the Delta region from garden to field agriculture occurred in the 20th century.

With the advent of electric pumps in 1905 and 1906, the previously used steam-powered and horse-powered devices were largely abandoned.

Large-scale irrigation was initially delivered through tidal gates and drainage ditches. Irrigation in the lower Delta relied on siphons and gravity flow while water wheels, windmills and low-head pumps were used on higher alluvial tracts. Irrigation in the Delta did not reach its full fluorescence until 1898 when the levee around the Moss Tract was breached to admit water and a steamer pumped water onto Rough and Ready Island (Thompson, 1957).

Settlements in the Delta were initially situated on naturally formed levees created by the merging of floodplains and tidal environments and consisted of single-family farms and farm labor camps. However, in the central Delta, sediments consisted primarily of peat and the natural levees were poorly developed.

The first levees in this area were built by crews of Chinese laborers using only shovels and wheelbarrows.

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San Joaquin County, CA Affected Environment and Environmental Consequences After the development of a clamshell dredger in the late 1800s, larger, more stable levees were constructed and agriculture expanded (McElhiney, 1992). The early levees and even later structures built in the 1860s and 1870s rarely remained intact for more than 1 or 2 years and required frequent repairs and upgrades.

Dredges were being widely used by 1870 and allowed for the use of a wider variety of fill materials, such as clay from the channel floors, in levee construction. In addition to these themes, the city of Stockton also underwent significant urban development within and adjacent to the study area. This was highly dependent on the development of shipping capacities at the Port of Stockton.

Methods for Identification
This study was limited to a record search and reconnaissance site visits to recorded sites within 1000 feet of the alignments in the northern portion of the study area, excluding the elements associated with Old Mormon Slough and RD 17. A small segment (2700 feet) along Duck Creek was identified as part of the study area after the record search was completed, but will be included during future studies in accordance with the PA. The record search was completed in April 2014. The site locations were then digitized and reconnaissance site visits were performed for a selection of those sites, including both prehistoric and historic sites. Sites visited were selected based on these factors:
 Age
 Site Type
 Accessibility
 Eligibility
An attempt to visit the locations of all prehistoric sites was made; however, certain prehistoric site locations were not accessible at the time of the field visit. Other site types targeted include historic buildings and structures and historic archaeological sites. Sites excluded from selection include historic linear alignments such as levees, roads and railroads, given their consistent appearance. Additionally, no attempt to visit structures associated with the Naval Supply Annex Stockton Historic District (NSAS-HD) located on Rough and Ready Island, was made as these buildings have previously been found eligible for the register and mitigation completed in the form of a Historic American Building Survey (HABS). Photographs of the Rough and Ready Island waterfront along the project corridor were taken. Because rights of entry were not available for the properties, all observations were made from the crown of the levee. A total of six cultural resources within Alternative 7A (Recommended Plan) were visited on April 24, 2014 and were completed by Nikki Polson, M.A., USACE Archaeologist and Stefanie Adams, USACE Cultural Resources Staff (Polson and Perry, 2014). Sites visited are noted in Table 5-44. Additional surveys and other necessary work will be completed as per the PA.

Known Cultural Resources
A total of 32 previously conducted archaeological investigations occurred within the Alternative 7a (RP) study area. This includes archaeological surveys, test excavations, data recovery projects and other investigations. At least 30 cultural resources were previously recorded in the Alternative 7a (RP) study area.

In addition to these resources, an isolated Native American burial was removed; 8 historic structures are listed, but not mapped in the Historic Property Data File; and 8 additional bridges were identified in the Caltrans Bridge Inventory within the study area. Cultural resources within or adjacent to the study area include prehistoric sites, levees, water conveyance structures, railroads, bridges and historic structures. A portion of the Naval Supply Annex Stockton Historic District (NSAS-HD) is located within the study area.

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San Joaquin County, CA Affected Environment and Environmental Consequences (RP) was determined. Consultation concerning the eligibility of cultural resources for the NRHP and effects to historic properties will occur as stipulated in the PA. All recorded sites are summarized in Table 5-44.

Prehistoric Sites
A total of 3 prehistoric sites were previously recorded within the study area. Each was recorded as an occupation site and most are known to contain or have once contained human remains. There is an additional known unrecorded site that will be investigated. Based on visits to 2 of the 4 sites and previous site recordation, the overall integrity of these sites is highly suspect as all were subject to disturbance through some degree of modern development, including development of subdivisions and a gravel pit.

Because of the nature of these sites, it is likely that additional prehistoric cultural resources and burials will be discovered during project implementation.

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San Joaquin County, CA Affected Environment and Environmental Consequences Table 5-44: Recorded Cultural Resources within Alternative 7a (RP) Site Number Site Type/Name Site Age
Visited
Yes/No Eligibility
P-39-0112 Atchison, Topeka and Santa
Fe Railroad Historic No Not Determined
P-39-0220 Occupation Site Prehistoric Yes Not Determined P-39-0237 Occupation Site Prehistoric Yes Not Determined P-39-0244 Bear Creek Prehistoric No Not Determined
P-39-0425 Entry Gate, NSAS-HD Historic No Contributing Element, Mitigated P-39-0427 Marginal Wharf, NSAS-HD Historic No Contributing Element, Mitigated P-39-2513 Bridge Historic No Not Eligible
P-39-2824 Bridge, NSAS-HD Historic No Contributing Element, Mitigated P-39-2864 Railroad, NSAS-HD Historic No Contributing Element, Mitigated P-39-2865 Railroad Bridge, NSAS-HD Historic No Contributing Element, Mitigated P-39-4269 House Historic No Recommended Not Eligible
P-39-4270 House Historic No Not Determined
P-39-4399 Mokelumne Aqueduct Historic Yes Recommended Eligible P-39-4516 Levee Historic No Not Determined
P-39-4517 Levee Historic No Not Determined
P-39-4576 Naval Supply Annex
Stockton Historic District Historic Yes Eligible, Mitigated P-39-4854 Central United Methodist
Church Historic Yes Recommended Eligible
P-39-4917 Shima Tract Levee Historic No Not Determined
P-39-4918 Mosher Slough Levees Historic No Not Determined P-39-4922 Brookside Levee Historic No Not Determined
P-39-5152 Burns Cutoff Levee (Left
Bank) Historic No Recommended Not Eligible
NA Unrecorded Burial Prehistoric No Not Determined
Unrecorded Section
of P-39-00098 Union Pacific Railroad Historic No Not Determined NA Unrecorded Railroad Spur Historic Yes Not Determined Bridge 29C-058 Historic No Not Eligible
Bridge 29C-096 Historic No Not Eligible
Bridge 29C-134 Historic No Not Eligible
Bridge 29C-140 Historic No Not Eligible
Bridge 29C-141 Historic No Not Eligible
Bridge 29C-239 Historic No Not Eligible
Bridge 29C-240 Historic No Not Eligible
Bridge 29C-243 Historic No Not Eligible
Bridge 29C-399 Historic No Not Eligible
Bridge 29-C400 Historic No Not Eligible
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San Joaquin County, CA Affected Environment and Environmental Consequences Water Conveyance
Portions of the Mokelumne Aqueduct and associated features are located within the study area. The aqueduct was recommended as eligible for listing in the NRHP under Criterion A for its association with the development of the east San Francisco Bay and Alameda and Contra Costa Counties. It was also recommended eligible under Criterion C as an example of the work of master engineer Arthur Powell Davis.

The system is still regularly maintained and fully operational.

Railroads
A portion of the Atchison, Topeka and Santa Fe Railroad intersects the project area. The section of the railroad in the study area has yet to be recorded or evaluated for its eligibility for listing in the NRHP. A complex of railroad lines on Rough and Ready Island is discussed under the NSAS-HD.

Historic Structures
Three sites with historic structures were previously recorded within the study area, including the Central United Methodist Church, which was recommended eligible for listing in the NRHP under Criterion C for its architecture and engineering. The associated school building was recommended not eligible for listing in the NRHP as its architectural style is well represented in the Central Valley. The remaining two structures are houses. One has been recommended not eligible for listing in the NRHP and the second remains unevaluated.

Bridges
Eleven bridges were recorded within the study area. All were listed as not eligible by CalTrans.

Historical Archaeological Site
A single historical archaeological site, P-39-0342, was recorded in the study area. It is a trash scatter. The site was determined not eligible for listing in the NRHP in 2000.

Naval Supply Annex Stockton Historic District (NSAS-HD) The remaining six resources are associated with the NSAS-HD. One of the recorded resources refers to the entire district, P-39-4576. P-39-4576 is the NSAS-HD located on Rough and Ready Island and occupies nearly 1500 acres. The NSAS-HD is organized as an orthogonal grid of streets oriented to the cardinal directions, with a network of rail line overlying the street grid. Buildings within the district include 38 warehouses, 9 transit sheds and open storage areas, as well as utilitarian and personnel support buildings.

Open areas around the periphery of the grid were also used as storage capabilities of the island. The railroad network includes a holding and reassignment yard and a classification yard. Spurs run from the rail yards to every warehouse and transit shed, as well as open storage areas. Only a portion of the NSAS-HD is located within the study area, including an entry gate, marginal wharf, vehicle bridge, the railroad spurs and railroad bridge (Table 5-44). The historic district was determined eligible for listing in the NRHP under Criteria A and C for its role in supplying the fleet during World War II and as an important example of new warehouse design developed during World War II. Because the operation of the historic district was being transferred from the Navy to the Port of Stockton and may cause adverse effects to the NRHP eligible site, HABS documentation was completed under Section 110(b)(2)a pursuant to a Memorandum of Agreement in 1998 (HABS No. CA-682).

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San Joaquin County, CA Affected Environment and Environmental Consequences Consultation
During the preconstruction engineering and design phase of the project, if authorized, USACE would then do a site-specific analysis including site-specific engineering and full site surveys in accordance with the processes set up in the PA. USACE shall prepare supplements to either draft or final environmental impact statements if: (1) USACE makes substantial changes in the proposed action that are relevant to environmental concerns; or (2) there are significant new circumstances or information relevant to environmental concerns and bearing on the proposed action or its impacts. If necessary, USACE would reinitiate Section 106 consultation with the State Historic Preservation Office (SHPO) and the Tribes to address any potential change in impacts.

State Historic Preservation Officer
USACE determined that the proposed undertaking would likely result in adverse effects to historic properties. Substantial portions of the APE have either not been surveyed or have been surveyed over five or even 10 years ago. USACE has prepared and initiated consultation concerning a PA with SHPO and Native American Tribes to guide the Section 106 process during project implementation. Before any ground disturbing activities commence, complete archaeological and historic building surveys would be completed as necessary. The PA has stipulations to address the identification and evaluation of cultural resources and development and implementation of historic property treatment plans (HPTPs). Specific mitigation measures would be developed in accordance with the PA to address any adverse effects on historic properties. A draft of the PA was submitted to SHPO on December 16, 2013. Comments from SHPO were received March 5, 2014. A copy of the draft PA can be found in the Engineering Addendum. The PA was executed by USACE and SHPO on May 11, 2016.

Native American Consultation
A list of potentially interested Native Americans was obtained from the District Native American Coordinator at Caltrans District 10 in Stockton. Two letters were sent to the Ione Band of Miwok Indians, the Buena Vista Rancheria of Me-Wuk Indians, the Wilton Rancheria, the Nototomne/Northern Valley Yokuts and the California Valley Miwok Tribe.

The first letter, dated August 12, 2012, informed them of the new feasibility study and requested any information they may have on areas of traditional cultural interest to their tribal members. There were two responses. Ms. Sylvia Burley, Tribal Chairperson of the California Valley Miwok Indians, requested Government to Government consultation which was forwarded to Mr. Mark Gilfillan, the USACE Tribal Liaison. Ms. Katherine Perez, Tribal Chairwoman for the Nototomne/Northern Valley Yokuts, called to request more information.

The first letters were sent out on December 2, 2013, including a description, location maps of the final array of alternatives, and a copy of the draft PA for review. A call from Mr. Randy Yonemura concerning the PA was received in December 2013; however, no specific comments have been submitted by any Tribe.

Since the first letters were sent out, USACE developed a revised draft Programmatic Agreement (PA) for the project. A second round of letters were sent on March 18, 2016 with a copy of the revised draft PA for review. No comments were received from the Tribes regarding the revised draft PA.

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San Joaquin County, CA Affected Environment and Environmental Consequences A final draft of the PA was distributed to tribes on August 13, 2014. In response, a letter from the California Valley Miwok Tribe stating they had no further comments and were requesting concurring party status was received on August 15, 2014. Ms. Perez called USACE for additional information, stated that she was very concerned about the possibility of human burials within the project area, and requested concurring party status. She chose to sign the final draft form of the document and submitted it via facsimile on August 20, 2014. USACE received comments concerning the project and PA from the Buena Vista Rancheria on August 29, 2014. USACE has provided the Buena Vista Rancheria responses to their comments in May 2016.

The United Auburn Indian Community expressed interest in this project on November 23, 2015 and have since been included in consultations.

The Draft Integrated Report was provided, and the Final Integrated Report will be provided to, the following Tribes: Wilson Rancheria, Nototomne/Northern Valley Yokuts, Californian Valley Miwok Tribe, Ione Band of Miwok Indian, United Auburn Indian Community, and Buena Vista Rancheria Me-Wuk Indians.

A PA has been signed by USACE and SHPO on May 11, 2016 as part of the submittal of this document.

ASSESSMENT METHODS AND BASIS OF SIGNIFICANCE
Assessment Methods
Analysis of the potential impacts was based on evaluation of changes to historic properties within the study area that may result from implementation of the project. The term “historic property” refers to any cultural resource that has been found eligible for listing or is listed, in the NRHP. Section 106 of the NHPA outlines the process in which Federal agencies are required to determine the effects of their undertakings on historic properties. In making a determination of the effects to historic properties, consideration was given to:
 Specific changes in the characteristics of historic properties in the study area.  The temporary or permanent nature of changes to historic properties and the visual study area around the historic properties.
 The existing integrity considerations of historic properties in the study area and how the integrity was related to the specific criterion that makes a historic property eligible for listing in the NRHP.

Basis of Significance
Effects to cultural resources would be from four types of construction related actions: (1) effects to the integrity of the visual and physical setting of historic properties; (2) effects to the structural integrity of historic buildings and structures from demolition; (3) effects from earth moving activities; and (4) effects from clearing, grubbing and follow-on planting.

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San Joaquin County, CA Affected Environment and Environmental Consequences Any adverse effects on cultural resources that are listed or eligible for listing in the NRHP (i.e., historic properties) are considered to be significant. Effects are considered to be adverse if they:
 Alter, directly or indirectly, any of the characteristics of a cultural resource that qualify that resource for the NRHP so that the integrity of the resource's location, design, setting, materials, workmanship, feeling or association is diminished.
 Additionally, according to CEQA, a project that may cause a “substantial adverse change” in the significance of a “historical resource” or a “unique archaeological resource” may have a significant impact on the environment (State CEQA Guidelines Section 15064.5, PRC 21083.2). CEQA defines a “substantial adverse change” as follows:
 Physical demolition, destruction, relocation or alteration of the resource or its immediate surroundings such that the significance of a historical resource would be materially impaired.  Demolition or material alteration in an adverse manner of those physical characteristics of a historical resource which convey its historical significance and justify its inclusion in or eligibility for inclusion in the California Register of Historical Resources, inclusion in a local register pursuant to Section 5020.1(k) of the PRC or its identification in a historical resources survey meeting the requirements of Section 5024.1(g) of the PRC.  Disturb any human remains, including those interred outside of formal cemeteries.

ALTERNATIVE 1 - NO ACTION
Under NEPA, this alternative reflects the expected future conditions without this project. Under CEQA, it reflects the existing condition at the time the Notice of Preparation was published (January 2010) and what would be reasonably expected to occur in the foreseeable future if the project was not approved. Levee erosion and seepage would continue. Historic properties currently behind the existing levees may be affected in the event of a levee failure and impacts would be significant and unavoidable.

ALTERNATIVE 7A
Alternative 7a has the potential to adversely affect cultural resources during placement of cutoff walls, seepage berms, deep soil mixing, levee raises and closure structures. The records and literature search, reconnaissance survey and the regional history of the area indicate that there are at least 30 previously recorded cultural resources and high potential for additional unknown historic properties within the study area. In particular, the prehistoric overview and previously recorded prehistoric sites suggests that there is a high probability that multiple prehistoric villages on the SJR and tributaries would be affected. The likelihood is also high for additional historic-era structures and features within the project. It is likely that historic properties will be adversely affected by this alternative. Effects to cultural resources under this alternative would be significant and unavoidable.

ALTERNATIVE 7B
Alternative 7b would incorporate the same proposed methods along the same levee elements as Alternative 7a, with the added improvements to RD 17. At least 30 cultural resources were previously recorded within or adjacent to the study area. The addition of RD 17 would likely result in more resources located within the study area. A record search was not performed within RD 17 and given the similarity of riverside environment, it is likely that a similar number of historic and prehistoric resources are located in or near the study area. Historic properties are likely to be adversely impacted by this alternative. Implementation of mitigation for effects to cultural resources under this alternative would reduce impacts, but would remain significant and unavoidable.

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San Joaquin County, CA Affected Environment and Environmental Consequences ALTERNATIVE 8A
Alternative 8a would encompass the same proposed methods for reducing flood risk as Alternative 7a over an increased number of levee miles. At least 44 cultural resources were previously recorded within or adjacent to the study area. The increased length of the project area would result in a greater likelihood for additional resources to be located within the study area. In particular, the prehistoric overview and previously recorded prehistoric sites suggests that there is a high probability that multiple prehistoric villages on the SJR would be affected. Historic properties are likely to be adversely impacted by this alternative. Implementation of mitigation for effects to cultural resources under this alternative would reduce impacts, but would remain significant and unavoidable.

ALTERNATIVE 8B
Alternative 8b would incorporate the same proposed methods along the same levee elements as Alternative 8a, with the added improvements to RD 17. At least 44 cultural resources are known to be within or adjacent to the study area. The addition of RD 17 would likely result in more resources located within the study area.

A record search was not performed within RD 17 and given the similarity of riverside environment, it is likely that a similar number of resources are located in or near the study area. Historic properties are likely to be adversely impacted. Implementation of mitigation for effects to cultural resources would reduce impacts, but would remain significant and unavoidable.

ALTERNATIVE 9A
Alternative 9a would incorporate the same proposed methods along the same levee elements as Alternative 7a, with the addition of channel improvements to create a bypass through Old Mormon Slough. At least 37 cultural resources were previously recorded within or adjacent to the study area. In particular, the prehistoric overview and previously recorded prehistoric sites, suggests that there is a high probability that multiple prehistoric villages on the SJR would be affected. A record search was not completed along Old Mormon Slough, but given the similarity of riverside environment, it is likely that a similar number of resources are located in or near the study area. The additional length of the project area could also result in a greater likelihood for additional resources to be located within the study area. Historic properties are likely to be adversely impacted by this alternative. Implementation of mitigation for effects to cultural resources would reduce impacts, but would remain significant and unavoidable.

ALTERNATIVE 9B
Alternative 9b would incorporate the same proposed methods along the same levee elements as Alternative 9a, with the addition to improvements to RD 17. At least 37 resources are known to be within or adjacent to the study area. The addition of RD 17 would likely result in more resources located within the study area.

A record search was not completed along Mormon Slough or RD 17, but given the similarity of riverside environment, it is likely that a similar number of resources are located in or near the study area. Historic properties are likely to be adversely impacted by this alternative. Implementation of mitigation for effects to cultural resources would reduce impacts, but would remain significant and unavoidable.

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MITIGATION
USACE began consultation concerning a PA with SHPO and Native American Tribes (Environmental Addendum). A fully executed PA will be in place prior to project implementation. Specific mitigation measures would be developed in accordance with the PA to address any adverse effects on historic properties through the development of an HPTP. The HPTP would guide the level of data recovery, mitigation or actions taken to resolve adverse effects to the historic property. The main requirements of the contents of a research design and HPTP are located in the PA.

Depending on the nature of the adverse effect, actions to protect or mitigate for adverse effects to historic properties may include the following:
 Redesigning the project to avoid historic properties or sensitive areas.  Conducting data recovery excavations of archaeological sites that cannot be avoided or are discovered during construction, based on an approved HPTP.  Monitoring all ground disturbing construction activities in areas where buried resources are anticipated.
 Surveying and protecting exposed inundated cultural deposits.  Protecting exposed archaeological sites from vandalism and erosion with fencing and revegetation or capping sites in an approved manner with appropriate material.  Preparing and implementing an inadvertent discovery plan.  If previously undiscovered resources are identified during an undertaking, suspend work while the resource is evaluated and mitigated to avoid any further impact.  Continue to consult with Native American or other groups to identify any traditional cultural properties or resource uses and address impacts.
 If human remains are discovered during any activities associated with bank protection measures, USACE, CVFPB and SJAFCA and their contractors will comply with State and Federal laws relating to the discovery and identification of human remains. In the case of Native American human remains found on non-Federal land, USACE and DWR will consult with the most likely descendant of the deceased regarding the disposition of human remains and associated burial items pursuant to the PA. This process includes contacting the coroner and developing a plan for the removal or protection of the remains pursuant to the PA.

Even with implementation of the PA, impacts to cultural resources would be significant and unavoidable.

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GROWTH INDUCEMENT
NEPA and CEQA require that an EIS and EIR discuss how a project, if implemented, could induce growth.

This section presents an analysis of the potential growth-inducing effects of the proposed project. Direct growth inducement would result if a project resulted in establishing a new demand for public services, facilities or infrastructure, such as the construction of new housing. Indirect growth inducement would result, for instance, if implementing a project would result in any of the following:
 Substantial new permanent employment opportunities (e.g., commercial, industrial or governmental enterprises);
 Substantial short-term employment opportunities (e.g., construction employment) that indirectly stimulates the need for additional housing and services to support the new temporary employment demand; and/or
 Removal of an obstacle to additional growth and development, such as removing a constraint on a required public utility or service (e.g., construction of a major sewer line with excess capacity through an undeveloped area).

DIRECT GROWTH EFFECTS
Construction activities associated with implementation of the LSJR Project would generate short-term employment. It is anticipated that there is sufficient workforce in the Stockton Metropolitan Area to support construction of the project, if approved. Because the existing labor force would be used, there would be no need for additional housing to be constructed and no new demand for public services, facilities or infrastructure. O&M of the project would not result in an increase in employees beyond current levels. If additional employees were needed, those jobs would be anticipated to be filled by the existing labor force.

Therefore, implementation of the LSJR Project would not directly induce growth as a result of an increase in population or in construction of new housing and associated support infrastructure.

INDIRECT GROWTH EFFECTS
Within the project area, population growth and urban development are driven by local, regional and National economic conditions. Between 2006 and 2011, the annual average population growth rate of San Joaquin County was 1 percent. The projected annual population growth rate for the county between 2012 and 2017 is anticipated to be 1.7 percent (San Joaquin County, 2010). Local land use decisions are within the jurisdiction of the Cities of Stockton, Lathrop and Manteca and San Joaquin County each who have adopted general plans, consistent with State law, that provide an overall framework for growth and development within their jurisdictions and the study area (including North Stockton, Central Stockton and RD 17). There are currently 15,500 acres of undeveloped land in the study area, including 12,800 acres in RD 17 and the remaining 2,700 acres in North and Central Stockton.

While each of the proposed alternatives improves levees to protect existing populations in the study area, Alternatives 7b, 8b, and 9b also would provide protection of currently undeveloped land in RD 17, therefore removing flood risk as an obstacle to growth. The magnitude of this potential impact was considered during project planning, including identification of the RP. EO 11988, Floodplain Management Analysis, is provided in Section 3.6. The Lower SJR Project Feasibility Study concluded that strengthening the existing system of levees, along with two closure structures, is the only practicable alternative to address FRM to the greatest population (located in North and Central Stockton), while minimizing induced development in the less populated RD 17.

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San Joaquin County, CA Affected Environment and Environmental Consequences reduced. Population growth associated with the urbanization of RD 17 would result in the physical development/expansion of housing, transportation systems, utilities and services, which could adversely affect the physical environment. As presented in Table 5-45, buildout of development projects in RD 17 would result in significant and unavoidable impacts including, but not limited to, conversion of prime farmland, criteria air pollutant emissions, increased light and glare, increased traffic congestion and increased noise levels. In addition, the cities worked together with San Joaquin County and other partners and Federal, State and local regulators to develop and approve the San Joaquin County Multi-Species Conservation and Open Space Plan (2000). This plan recognizes the planned urban development and defines a comprehensive plan for conserving and mitigating for impacts to sensitive natural resources.

USACE and SJAFCA lack the authority to approve or deny development projects or to impose mitigation to address significant environmental impacts due to land use decisions; that authority resides with the local cities and San Joaquin County. In addition, numerous Federal, State, regional and local agencies are specifically charged with protecting environmental resources and ensuring that planned development occurs in a sustainable manner. Together, these agencies exercise the authority to reduce the effects of development on the environment. However, development to accommodate population growth in RD 17 due to reduction in flood risk would still be expected to result in significant and unavoidable impacts.

CUMULATIVE EFFECTS
NEPA and CEQA require the consideration of cumulative effects of the proposed action combined with those of other projects. NEPA defines a cumulative effect as an environmental affect that results from the incremental effect of an action when combined with other past, present and reasonably foreseeable future actions, regardless of what agency (Federal or non-Federal) or person undertakes such other actions (40 CFR 1508.7). The CEQA Guidelines require an assessment of the cumulative impacts of a project when the project’s incremental effect is “cumulatively considerable.” CEQA requires cumulative impacts of a project be assessed with respect to past, current and probable future projects within the region. CEQA Guidelines (Section 15355) define cumulative effects as “two or more individual effects that, when considered together, are considerable or which compound or increase other environmental impacts.” According to CEQA Guidelines Section 15130 (b), the purpose of the cumulative impacts discussion shall reflect “the severity of the impacts and their likelihood of occurrence” and shall “be guided by the standards of practicality and reasonableness and should focus on the cumulative impact to which the identified other projects contribute...” As further defined in Section 15130 (b), an element necessary to an adequate discussion of significant cumulative impacts is a list of past, present and probable future projects producing related or cumulative impacts, including those projects outside the control of the Lead Agency (list approach); or a summary of projections contained in an adopted general plan or in a prior environmental document that was adopted or certified that described or evaluated regional or area-wide conditions contributing to the cumulative impact (plan approach). This cumulative analysis uses the list approach.

Section 5.23.3 includes a description of the past, present and future projects.

METHODOLOGY AND GEOGRAPHIC SCOPE OF THE ANALYSIS
Methodology
If a technical issue area includes a project-specific impact as a result of implementation of a proposed alternative, a cumulative context is presented. The cumulative impact analysis takes into consideration whether the projects identified in Section 5.23.3, in combination with each of the alternatives, would have the potential to affect the same resources. If there is not a combined effect, then a finding of no cumulative impact is made. If there would be a combined effect, then a determination is made if that combined effect would: (1) result in a significant cumulative impact; and (2) if a proposed alternative’s contribution to the effect would be considerable (consistent with CEQA Guidelines Section 15355).

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San Joaquin County, CA Affected Environment and Environmental Consequences Finally, a determination is made as to whether mitigation measures recommended for the project-specific impact would reduce the contribution to the cumulative impact to a less than significant level; therefore, resulting in a less than significant cumulative impact. Mitigation of significant cumulative effects could be accomplished by rescheduling actions of proposed projects and adopting different technologies to meet compliances. Significance of cumulative effects is determined by meeting Federal and State mandates and specified criteria identified in this document for affected resources.

Geographic Scope
The context of the cumulative analysis varies by technical issue area. The cumulative context for each technical issue area is further defined by the specific geographic area affected. Air and water resources extend beyond the confines of the project footprint since effects on these resources would not necessarily be confined to the project area. When the effects of the project are considered in combination with those of other past, present and future projects to identify cumulative effects, the other projects that are considered may also vary depending on the type of environmental effects being assessed. The following are the general geographic areas associated with the different resources being addressed in this analysis:

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San Joaquin County, CA Affected Environment and Environmental Consequences Table 5-45: Geographic Area That Would be Affected by the LSJR Project Resource Area Geographic Area
Land use and agriculture San Joaquin County, City of Stockton Hydrology and Hydraulics
The LSJR project area, with regional implications, including: SJR, Lower Calaveras River, Stockton Deepwater Ship Channel, Tenmile Slough, Fivemile Slough, Fourteenmile Slough, Mosher Slough and in the vicinity of the study
Water quality
The LSJR project area, with regional implications, including: SJR, Lower Calaveras River, Stockton Deepwater Ship Channel, Tenmile Slough, Fivemile Slough, Fourteenmile Slough, Mosher Slough and in the vicinity of the study
Vegetation
The LSJR project area, with regional implications, including:
individual construction sites and SJR, Lower Calaveras River, Stockton Deepwater Ship Channel, Tenmile Slough, Fivemile Slough, Fourteenmile Slough, Mosher Slough
Wildlife
The LSJR project area, with regional implications, including:
individual construction sites and SJR, Lower Calaveras River, Stockton Deepwater Ship Channel, Tenmile Slough, Fivemile Slough, Fourteenmile Slough, Mosher Slough
Fisheries
The LSJR project area, with regional implications, including:
individual construction sites and SJR, Lower Calaveras River, Stockton Deepwater Ship Channel, Tenmile Slough, Fivemile Slough, Fourteenmile Slough, Mosher Slough
Special-status species
The LSJR project area, with regional implications, including:
individual construction sites and SJR, Lower Calaveras River, Stockton Deepwater Ship Channel, Tenmile Slough, Fivemile Slough, Fourteenmile Slough, Mosher Slough
Fish and aquatic habitats
SJR system, Mosher Slough/Creek, Fourteenmile Slough, Tenmile Slough, Fivemile Slough, Calaveras River, Stockton Diverting Canal, Old Mormon Slough, French Camp Sough and the South Delta, with regional implications for species
Cultural resources Individual ground disturbance sites, with regional implications Transportation and
circulation
Roadway network within the study area, including Cities of Stockton, Manteca, Lathrop and western portion of San Joaquin County, with regional implications
Air quality Regional (SJCAPCD); global for GHG emissions Noise Immediate vicinity of the individual sites of construction activity and haul routes.

Recreation Local (facilities near construction sites)
Visual resources Individual levee improvement sites and landscape level Hazards and hazardous
materials Individual construction and other ground disturbance sites SJCAPCD = San Joaquin County Air Pollution Control District

LSJR PROJECT IMPACTS
The potential impacts from implementing the LSJR project are summarized inTable ES-5. Significant and unavoidable impacts from implementing the RP, Alternative 7a, are shown in Table 5-45.

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PAST, PRESENT AND REASONABLY FORESEEABLE FUTURE PROJECTS This section briefly describes the past, present and future projects in the LSJR study area. The exact construction timing and sequencing of these projects are not yet determined or may depend on uncertain funding sources. A forecast of projects likely to be constructed concurrently with the proposed project is required to evaluate cumulative effects on environmental resources in the area. In addition, mitigation or mitigation measures must be developed to avoid or reduce any adverse effects to less than significant based on Federal and local agency criteria. Those effects that cannot be avoided or reduced to less than significant, are more likely to contribute to cumulative effects in the area.

Projects with a FRM Emphasis
The following descriptions of related or similar FRM projects include those that are under active consideration, were proposed or have some form of environmental documentation completed. In addition, these projects have the potential to affect the same resources and fall within the same geographic scope and are thus to be cumulatively considered. In particular, the affected resources are biological resources (riparian habitat, wildlife disturbance), agriculture, air quality and GHGs (climate change), hydrology and geomorphology. See Table 5-45 for the geographic scope of consideration for effects on those resources.

Delta Flood Emergency Facilities Improvement Project
Recovery from catastrophic failure of Delta levees will be undertaken by the State of California, if necessary, to manage salinity for the environment and human use, which will also protect the brackish Suisun Marsh. As described in DWR’s Delta Flood Emergency Facilities Improvement Project, the State is working to ensure that it has the appropriate infrastructure and supplies in the Delta to respond to and recover quickly and effectively from, major flood or earthquake disasters in the Delta. Locations of storage and transfer sites for stockpiled flood fight materials are identified:
 Establish two new material storage and transfer facility sites:
 Stockton West Weber Avenue; and
 Brannan Island State Park.
 Modify an existing material storage 5.23.3 facility at Rio Vista.  Establish new flood fight supply facilities at all three locations.  Make site preparations to support Incident Command Posts at Stockton West, Weber Avenue and Brannan Island State Recreation Area.
 In addition to the 223,000 tons of quarry rock stockpiled by DWR at Rio Vista and within the Port of Stockton, DWR would also stockpile up to 40,000 tons of quarry rock material of variable gradations less than 24-inch-minus at Stockton West, Weber Avenue and Brannan Island and 20,000 tons of sand in Rio Vista for a total additional increment of 100,000 tons.

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San Joaquin County, CA Affected Environment and Environmental Consequences Designated Floodway Program
The CVFPB of the State of California administers the Designated Floodway Program, which addresses land use management within the floodway. This program provides a nonstructural way to keep development from encroaching into flood-prone areas. It also reduces future potential flood damages by preserving the reasonable flood passage capacities of natural watercourses. The CVFPB controls the Designated Floodway Program by adopting floodway boundaries, developing plans for modifications of boundaries and approving changes in acceptable use and types of structures within the floodways. Designated Floodway refers to the channel of the stream and that portion of the adjoining floodplain reasonably required to provide for the passage of a design flood. It is also the floodway between existing levees as adopted by the CVFPB (formerly the Reclamation Board) or the Legislature. Floodways in the study area are primarily limited to the areas between levees.

Federal Emergency Management Agency (FEMA), Flood Mitigation Assistance Program and the Hazard Mitigation Grant Program
These programs seek to reduce or eliminate the loss of life and property damage resulting from natural and human-caused hazards. In order to qualify for these programs, a community must be enrolled in the NFIP and have a Flood Mitigation Plan approved by the FEMA Regional Director. This plan must include a description of the existing flood hazard and identification of the flood risk including estimates of the number and type of structures at risk, repetitive loss properties and the extent of flood depth and damage potential.

A project must be cost-effective, not costing more than the anticipated value of the reduction in both direct damages and subsequent negative impacts to the area if these programs must compete for the funding. The Cities of Stockton, Lathrop and Manteca are enrolled in the NFIP. San Joaquin County’s enrollment covers the unincorporated areas of the County, which includes the study area outside of the Stockton, Lathrop and Manteca city limits.

SJR Levee Stability Program
Reclamation District No. 17 Levee Seepage Area Project (LSAP) The RD 17 LSAP consists of 3 phases of levee repairs to remedy levee seepage within the RD 17 levee system.

Phase 1 Project. In RD 17, improvements to some levee reaches consisted of reconstruction and extension of landside levee toe berms with earth and gravel fill, both landward and along the levee toe so as to reduce seepage exit gradients to less than 0.5. Project proponents concluded that there was no NEPA trigger for the Phase 1 Project and this phase was found to be statutorily exempt from CEQA. The Phase 1 Project was found to be categorically exempt from CEQA because the work consisted of repairing existing public facilities, involved no expansion of use (CCR 15301) and consisted of reconstructing existing facilities located on the same site. In addition, the Phase 1 Project was found to be categorically exempt because the facilities were planned to have the same purposes and capacity (CCR 15302). The levee elements selected for the Phase I Project were chosen because these elements lacked any sensitive environmental resources that would potentially be affected by construction activities. The Phase 1 Project was completed in 2008.

Phase 2 Project. Consisted of repairs and improvements to additional levee segments in RD 17. Under CEQA, environmental impacts associated with the Phase 2 Project were addressed in the Initial Study/Proposed Mitigated Negative Declaration for the Phase II–RD 17 100 Year Levee Seepage Project (RD 17 2009). Project proponents determined that there was no NEPA trigger for the Phase 2 work.

Construction of the Phase 2 Project was completed in the summer of 2010.

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San Joaquin County, CA Affected Environment and Environmental Consequences Phase 3 Project. RD 17 is the lead agency for Phase 3 of the LSAP. A variety of levee improvements are being considered for the Phase 3 Project, including construction of seepage berms and setback levees, installation of slurry cutoff walls and chimney/blanket drains and improvements to dry land levees to reduce under seepage and through seepage gradients. Proposed levee improvements would occur along various sections of the RD 17 levee system starting near the southern boundary of the city of Stockton, through the city of Lathrop and to the western boundary of the City of Manteca. RD 17 initiated this effort in cooperation with DWR, CVFPB, USACE with the aim of reducing flood risk during a flood with a 1 percent chance of occurring in any given year or 0.01 AEP. USACE will have a Section 408 and, potentially, a Section 404 decision on this project. Section 408 authority and approvals are in Section 5.23.4. A Draft EIS/EIR for this project was prepared and circulated in September 2011. The Final EIS has not been released.

Paradise Cut
Calif & LLC/Cambay group is planning the Paradise Cut project. Improvements to Paradise Cut associated with the River Islands at Lathrop Project would increase floodwater conveyance capacity and storage capacity of Paradise Cut. These actions would be consistent with the South Delta Flood Conveyance Plan.

Central Valley Flood Protection Plan (CVFPP) of 2017
The State’s (DWR) comprehensive, system-wide plan for reducing flood risks to lands currently protected by the SJR Basin Flood Control Project lays out the State’s broad plan for the Central Valley. Through the 2017 CVFPP, DWR initiated the Regional Flood Management Planning effort to assist local agencies in developing long-term regional flood management plans. Plans should identify local needs, local and regional flood management priorities and establish a common vision for partners. The CVFPP identified nine regions (Upper Sacramento, Mid-Sacramento, Feather River, Lower Sacramento, Delta-North, DeltaSouth, Lower San Joaquin, Mid-San Joaquin and Upper San Joaquin), which have formed working groups led by a local agency and consists of representatives from flood management agencies, land use agencies, flood emergency responders, permitting agencies and environmental and agricultural interests. The regional plans will present local agencies' perspectives of flood management with a prioritized list of projects that need to be implemented to reduce flood risks in each region. Each plan will also present an assessment of the proposed project costs and benefits, considering the projects’ potential contributions to an integrated multi-benefit and basin-wide solution.

CALFED Levee System Integrity Program
The goal of the CALFED Levee System Integrity Program is to reduce risk to land use and associated economic activities, water supply, agriculture and residential use, infrastructure and the ecosystem from the effects of catastrophic breaching of Delta levees. Estimates predict that 520 miles of levees need modification and maintenance to meet the PL 84-99 standard for Delta levees. The program continues to increase levee stability throughout the Delta.

Delta Islands and Levees Feasibility Study
USACE’s Delta Islands and Levees Feasibility Study (Delta Study) is assessing ecosystem restoration opportunities and flood risk problems in the Delta area. A Draft FR/EIS was released for public review in April 2014, tentatively recommending 90 acres of intertidal marsh restoration in the central Delta. Pending reviews, the report would be finalized as an interim feasibility report that would make recommendations on construction projects and/or additional studies for authorization by Congress.

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San Joaquin County, CA Affected Environment and Environmental Consequences The Delta Plan
The Delta Plan was developed by the Delta Stewardship Council (DSC) and adopted on May 16, 2013. It became effective, with legally-enforceable regulations, on September 1, 2013. It is a long-term, comprehensive management plan designed to meet the 2 co-equal goals of providing a more reliable water supply for California and protecting, restoring and enhancing the Delta ecosystem. The Delta Plan generally covers 5 topic areas and goals: increased water supply reliability, restoration of the Delta ecosystem, improved water quality, reduced risks of flooding in the Delta and protection and enhancement of the Delta.

The DSC does not propose constructing, owning or operating any facilities related to these 5 topic areas.

Rather, the Delta Plan sets forth regulatory policies and recommendations that seek to influence the actions, activities and projects of cities, counties, State, Federal, regional and local agencies toward meeting the goals in the 5 topic areas.

The Delta Plan could contribute to beneficial cumulative effects by setting forth regulatory policies and recommendations that influence projects in a manner that would improve water quality, water supply reliability, FRM and increase habitat for fish and wildlife.

Navigation Projects
San Francisco Bay to Stockton Deep Water Ship Channel Deepening Project USACE, DWR and the Port of Stockton conduct annual maintenance dredging of the Stockton Deep Water Ship Channel. Annual maintenance dredging is performed to maintain the DWSC to authorized depths.

Fine sediments cause shoaling, which must be removed to maintain adequate depth for commercial shipping traffic using the navigation channels. Failure to perform maintenance dredging would result in unsafe conditions and a restriction to access to the Port of Stockton from the San Francisco Bay, both a substantial risk to human safety, as well as an economic harm to the Port and the commercial activities that use the Port’s facilities.

Dredged materials are removed by using a hydraulic cutter head suction dredge and a dragline and clamshell crane are used for rock placement. The material is then deposited at previously authorized Dredged Material Placement (DMP) sites. Dredge slurry is routed to the DMP sites via pipelines. DMP sites are diked and dredge slurry is allowed to settle and consolidate at these sites. Decant water is then discharged back into the waterway, from some sites, as determined during annual coordination. Dredged spoils are allowed to dry and remain stockpiled at the sites for periodic use for levee repairs, livestock grazing and other purposes.

Projects Affecting Fish and Wildlife That Use the Project Area As described in Sections 5.9, 5.10, 5.11 and 5.12, substantial long-term effects on vegetation, fish and wildlife are related to the removal of vegetation in compliance with the USACE levee vegetation management policy. Regarding wildlife, this could contribute to a cumulative effect when combined with other projects that adversely affect habitat for wildlife that use the vegetation on or near levees in the project area. Regarding fish, this could contribute to a cumulative effect when combined with other projects within the geographic range of the fish that would be affected. Thus, the FRM and navigation projects described above in Section 5.23.3 could also adversely affect the same species of fish or wildlife that would be affected by vegetation removal under the project. The projects described intend to improve habitat conditions for the natural environment and the plants and animals that depend upon it.

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San Joaquin County, CA Affected Environment and Environmental Consequences CALFED Ecosystem Restoration Program
The goals of the CALFED Ecosystem Restoration Program are to:
 Recover 19 at-risk native species and contribute to the recovery of 25 additional species.  Rehabilitate natural processes related to hydrology, stream channels, sediment, floodplains and ecosystem water supply.
 Maintain and enhance fish populations critical to commercial, sport and recreational fisheries.  Protect and restore functional habitats, including aquatic, upland and riparian, to allow species to thrive.
 Reduce the negative effects of invasive species and prevent additional introductions that compete with and destroy native species.
 Improve and maintain water and sediment quality to better support ecosystem health and allow species to flourish.

The Ecosystem Restoration Program, which is divided into the San Joaquin, Sacramento and Delta and Eastside tributary regions, includes the following kinds of actions:
 Develop and implement habitat management and restoration actions, including restoration of river corridors and floodplains, reconstruction of channel-floodplain interactions and restoration of Delta aquatic habitats.
 Restore habitat that would specifically benefit one or more at-risk species.  Continue major fish screen projects and conduct studies to improve knowledge of their effects.  Restore geomorphic processes in stream and riparian corridors.  Implement actions to improve understanding of at-risk species.  Develop understanding and technologies to reduce the effects of irrigation drainage on the SJR and reduce transport of contaminant (selenium) loads carried by the San Joaquin to the Delta and the Bay.
 Implement actions to prevent, control and reduce effects from nonnative invasive species.

Ecosystem Restoration Program actions contribute to cumulative beneficial effects on fish and wildlife species, habitats and ecological processes.

California Water Fix
On April 30, 2015, Governor Brown and Federal officials announced that they are proposing a new Bay Delta Conservation Plan (BDCP) sub-alternative, Alternative 4A, that would replace BDCP Alternative 4 (the proposed BDCP) as the State’s proposed project. Alternative 4A reflects the State’s proposal to separate the conveyance facility and habitat restoration measures into 2 separate efforts: California WaterFix and California EcoRestore. California EcoRestore, the primary habitat restoration program, would be overseen by the California Natural Resources Agency and implemented under the California Water Action Plan. These 2 efforts are a direct reflection of public comments and fulfill the requirement of the 2009 Delta Reform Act to meet the co-equal goals. DWR and the USBR prepared a partially Recirculated Draft Environmental Impact Report/Supplemental Draft Environmental Impact Statement (RDEIR/SDEIS) that addresses the impacts of Alternative 4A. The RDEIR/SDEIS includes those portions of the DEIR/DEIS (for the BDCP) that were amended or supplemented based on comments received and changes in impact analysis warranting another public review prior to publication of final documents.

Long Term Central Valley Project (CVP) BOs
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San Joaquin County, CA Affected Environment and Environmental Consequences BOs issued by USFWS and NMFS for CVP and the SWP determined that the existing fish passage structure at Fremont Weir was inadequate to allow normal fish passage at most operational levels of the Sacramento River. As a result, BOs required the USBR and/or DWR to increase inundation of suitable acreage for fish habitat within the Yolo Bypass and to modify operations of the Sacramento Weir or Fremont Weir to increase juvenile rearing habitat. The BOs also require restoration of 8,000 acres of tidal marsh habitat in the Delta to benefit Delta smelt and up to 20,000 acres of salmonid habitat restoration. The operations of the SWP and CVP are currently subject to the terms and conditions of these BOs until the new water conveyance infrastructure identified in the BDCP becomes operational. At that time, an integrated BO on coordinated long-term operation of the CVP and SWP will be completed by USFWS and NMFS.

Implementation of the BOs is expected to be compatible with the LSJR project.

SJR Restoration Program
The USBR, USFWS, NMFS, DWR, DFG and Cal EPA are participating in the SJR Restoration Program.

The goal of the program is to restore and maintain fish populations in the mainstem of the SJR below Friant Dam to the confluence of the Merced River and to reduce or avoid adverse water supply impacts on all of the Friant Division long-term contractors. The SJR Restoration Program involves operation of Friant Dam and downstream flow-control structures to release flows to the SJR and diversion of surplus water during wet hydrologic conditions to the Friant- Kern and Madera canals.

U.S. Department of Agriculture, NRCS Wetland Reserve Program California’s Wetlands Reserve Program focused on the restoration of a variety of wetland types throughout the State, including seasonal wetlands, semi-permanent marshes and vernal pools along the perimeter of the Central Valley, riparian corridors and tidally-influenced wetlands. The Wetland Reserve Program was used to restore land along the SJR that has experienced flooding.

USFWS, SJR National Wildlife Refuge
The SJR National Wildlife Refuge is located within the historic floodplain of the confluences of the San Joaquin, Stanislaus and Tuolumne Rivers and downstream from the confluence with Orestimba Creek.

Refuge lands consist of oak-cottonwood-willow riparian forest, pastures, agricultural fields and wetlands.

This refuge was established in 1987 under authority of the ESA, the Land and Water Conservation Fund Act and the Migratory Bird Conservation Act. The original 1,638 acre refuge has grown tremendously through recent land acquisitions to 6,642 acres within an approved refuge boundary of 12,877 acres.

USFWS, San Luis National Wildlife Refuge
This 26,609-acre refuge is a mixture of managed seasonal and permanent wetlands, riparian habitat associated with 3 major watercourses and native grasslands/alkali sinks/vernal pools. This refuge primarily provides habitats for migratory and wintering birds. The largest concentration of mallards, pintails and green-winged teal in the San Joaquin Valley are found here. One of only 22 herds of the indigenous Tule elk is located here, as are a variety of endangered, threatened and sensitive species.

Development Projects.

Table 5-46 are within RD 17 boundaries in the Cities of Manteca, Stockton, Lathrop and in unincorporated areas of San Joaquin County.

ATTACHMENT D 1417
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San Joaquin County, CA Affected Environment and Environmental Consequences San Joaquin County Development Projects
Development projects in the sphere of influence of Stockton, Manteca and Lathrop that have the potential to affect similar resource areas such as biological resources, air and noise, have been included for analysis.

Table 5-46: Development Projects within RD 17
Jurisdiction
Date Approved/
Anticipated Location Size
Major Environmental
Impacts
City of Lathrop
Mossdale
Landing1,2
Much of the
overall
development is
complete.

West of I-5,
adjacent SJR in
RD 17
1,7000 units +
commercial space
West Lathrop Specific
Plan Draft
Environmental Impact
Report (City of Lathrop
1995:K-4)
Significant Unavoidable
Impacts
Loss of Prime Farmland
Increase in regional
criteria air pollutant
emissions
Increase in light and
glare
Increase in traffic
congestion
Increased potential for
flood damage
Mossdale
Landing
East1,2
Much of the
overall
development is
complete.

West of I-5,
adjacent SJR in
RD 17
430 units +
commercial space
Mossdale
Landing
South1,2
Much of the
overall
development is
complete.

West of I-5,
adjacent SJR in
RD 17
450 units +
commercial space
Central
Lathrop
Specific
Plan1
Entitlements
approved in
2004, annexed in
20053
. Some
utilities and
roadways
installed. No
structures in
place. No
immediate plans
for further
construction.

West of I-5,
adjacent to SJR in
RD 17 (north of
Mossdale
Landing)
6,800 units + 5
million sq. ft.
office and
commercial
Central Lathrop specific
Plan Draft
Environmental Impact
Report (City of Lathrop
2004: 7-1; 7-5)
Significant Unavoidable
Impacts
Deficient level of service
at intersections and
highway segments
Increase in regional
criteria air pollutants
during construction
period
Increase in long-term
regional emissions
Increase in traffic noise
levels by 3 dBA or more
Noise levels would
exceed city’s “normally
acceptable” land use
compatibility standards
ATTACHMENT D 1418
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San Joaquin County, CA Affected Environment and Environmental Consequences Jurisdiction
Date Approved/
Anticipated Location Size
Major Environmental
Impacts
Loss of Important
Farmland in categories of
Prime, Statewide and
Local Importance
River Islands River Islands is
currently
working with the
State and
Federal agencies
to finalize the
permits needed
to begin
development.
(City of Lathrop
2010).

Stewart Tract
(bounded by
Paradise Cut, SJR
and Old River;
north of I-205 and
west of the SJR
Up to 11,000
units _ 2 golf
courses, 45-acre
town center, boat
docks, 260 acres
of parks, 600
acres of lakes and
waterways, 600
acres of open
space (City of
Lathrop 2002).

Includes
improvements to
Paradise Cut (a
flood control
bypass),
consistent with
the South Delta
Flood
Conveyance Plan
Draft Environmental
Impact Report for the
River Islands at Lathrop
Project (City of Lathrop
2002: 2-9 to 2-77).

Significant Unavoidable
Impacts
Degradation of freeway
and ramp operations on I205
Degradation of freeway
and ramp operations on I5
Increases in long-term
regional emissions
Odors associated with
water reclamation plants
Conversion of 3,620
acres of Important
Farmland in the Prime
and Statewide
Importance categories
Cancellation of up to
1,770 acres of
Williamson Act contracts
South
Lathrop
Specific
Plan4
Pending –
NOP/IS issued
in 2006.

South of SR 120
at I-5/SR 120 split
689 acres GPA,
prezone,
annexation and
SP
Environmental Review is
pending
City of Manteca
ATTACHMENT D 1419
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San Joaquin County, CA Affected Environment and Environmental Consequences Jurisdiction
Date Approved/
Anticipated Location Size
Major Environmental
Impacts
Trails
Project5
Environmental
review process is
beginning.

Southwestern
portion of
Manteca,
southwest of the
intersection of
West Woodward
Avenue and
McKinley
Avenue. Adjacent
to the dry land
levee and near
Oakwood Shores.
477 acres, 1,651-
unit residential
development
Environmental review is
pending
Terra Ranch5 Tentative map
application has
been submitted.

Environmental
review process is
beginning.

Southside of West
Woodward
Avenue, one-half
mile west of
Airport Way;
southern boundary
is adjacent to the
dry land levee
Approx. 66 acres,
209 unit
residential
development
Environmental review is
pending
Macado5 The
environmental
impact report
has been
certified. No
application to
LAFCo has been
made; approval
of tentative map
is pending.

Southwest corner
of West
Woodward
Avenue and
Airport Way;
Southern
boundary is
adjacent to the dry
land levee
Approx. 155
acres, 590 unit
residential
development
Draft Environmental
Impact Report for
Machado Estates Vol. I
(City of Manteca 2007:

ES-5; 3-12)
Significant Unavoidable
Impacts
Conversion of Prime
Farmland, Unique
Farmland, Farmland of
Statewide Importance
(59.9 acres) pg 3-12
Increase in emissions of
criteria pollutants
Unacceptable LOS on
freeway ramps and
mainline segments and
local roadways
City of Stockton
Weston
Ranch
Towne
Center
Project1,6
City Council
approved
December 2,
2008. Much of
overall
development is
complete.

West side of I-5,
north side of
French Camp
Road
500,000 sq. ft
large-scale retail,
210,000 sq. ft
retail: shops,
restaurants,
commercial
Weston Ranch Towne
Center Mitigation
Monitoring and
Reporting Program (City
of Stockton 2008)
Significant and
Unavoidable Impacts
ATTACHMENT D 1420
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San Joaquin County, CA Affected Environment and Environmental Consequences Jurisdiction
Date Approved/
Anticipated Location Size
Major Environmental
Impacts
Conversion of Prime
Farmland (42.24 acres)
Deficient level of service
at Mathews Road/I-5
ramp
Traffic impacts at French
Camp Road/I-5
Interchange
Increase in emissions of
criteria air pollutants
San Joaquin County
Oakwood
Shores7
(Oakwood
Lake)
Approved and
partially
constructed.

Roads and
utilities in place,
but less than 10
housing units in
place. No
immediate plans
for further
construction.

South of SR
120/580 between
Lathrop and
Manteca
480 lots, 264
constructed;
approx. 45 will
be eliminated for
levee work4
Not Applicable: Former
sand and gravel
extraction site and former
site of Manteca
Waterslides; was
converted to lake and
resort community; went
into foreclosure in 2008
Notes: dBA = A-weighted decibels; I-5 = Interstate 5; GPA = general plan amendment; SP = specific plan; LAFCo = local agency formation commission; RD 17 = reclamation District No. 17; sq. ft. = square feet; SR 120 = State Route 120 1 City of Stockton 2006a:6-6 2 Mossdale Village Planning Area in the West Lathrop Specific Plan, approved in 2002
3 City of Lathrop 2010
4 South Lathrop Specific Plan: Notice of Preparation/Initial Study (City of Lathrop 2006)
5 Durrer, pers. Comm., 2010 6 Liaw. Pers. Comm., 2010
7 Griffin, pers. Comm., 2010
Source : Data compiled by AECOM in 2010
PROJECTS REQUESTING SECTION 408 APPROVAL
Non-Federal project partners desiring to modify Federal works must request permission from USACE under Section 14 of the Rivers and Harbors Act of 1899 (33 USC 408), referred to as “Section 408 permission.” A number of projects in the Central Valley recently received 408 approval and others may request it. Table 5-47 summarizes those that received a letter of permission under Section 408 or that are seeking a letter of permission to alter a Federal project. These projects are listed for context.

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San Joaquin County, CA Affected Environment and Environmental Consequences Table 5-47: Projects Requesting Section 408 Approval
Project Lead
Agency
Letter of
Permission
Date
Letter of Permission Issued
Cache Creek Setback Levee DWR CA 22-May-13
West Sacramento Levee Improvement Project - CHP WSAFCA 29-Jun-11 West Sacramento Levee Improvement Project -
Rivers WSAFCA 29-Jun-11
West Sacramento - I Street Bridge WSAFCA 2010
TRLIA - Bear River Setback Levee + UPIC TRLIA 19-Jun-06 TRLIA - Upper Yuba River Levee Improvement
Project TRLIA 24-Mar-11
TRLIA - Feather River Segment 2 TRLIA 12-Dec-06
TRLIA - Feather River Segment 1 and 3 TRLIA 3-Aug-07
TRLIA - Toe Road TRLIA 9-Jul-13
Natomas Levee Improvement Project - Natomas
Cross Canal, Phase 1 SAFCA 19-Jul-07
Natomas Levee Improvement Project - Sacramento
River, Phase 2 SAFCA 2/20/2009 & 5/22/2009
Natomas Levee Improvement Project - Natomas East
Main Drainage Canal, Phase 3 SAFCA 20-Apr-10
Natomas Levee Improvement Project - Sacramento
River, Phase 4a SAFCA 7-Mar-11
Feather River - Star Bend LD1 16-Jun-09
Mid Valley - Knights Landing Ridge Cut KLRDD 17-Apr-14
Anticipated Future Letters of Permission
RD 17 - Mossdale RD 17 2015
Southport WSAFCA 2015
River Islands City of
Lathrop 2017
California Water Fix DWR To be
determined

CUMULATIVE IMPACT ANALYSIS
The following describes the project’s potential contribution to cumulative effects on each resource topic presented in Sections 5.1 through 5.21.

Geology and Geomorphology
Other development in the study area would be subject to the same types of geology and geomorphology as the LSJR Project. However, these types of impacts represent site-specific effects and do not result in a greater combined impact than the individual impacts. Further, the proposed levees would continue to affect local geomorphological process similar to existing conditions and would not further alter the natural river meander or deposition. Therefore, no cumulative effect would occur.

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San Joaquin County, CA Affected Environment and Environmental Consequences Seismicity
Other development in the study area would be subject to the same seismic conditions as the LSJR Project.

Seismic hazards represent hazards to people and property on a site-specific basis and do not result in a greater combined impact than the individual impacts. Further, proposed facilities would be designed, constructed and maintained in compliance with the regulatory standards of USACE, CVFPB and the latest seismic design standards. As a result, levees, cutoff walls and floodwalls would be designed to avoid or minimize any potential for seismic-related failure. Thus, no cumulative effect would occur.

City Council and Concurrent AuthoritiesMay 23, 2023

City Council and Concurrent Authorities
May 23, 2023