Attachment D - Lower San Joaquin River Feasibility & Environmental — City Council and Concurrent Authorities, May 23, 2023 (part 1 of 3)

January 2018
San Joaquin River Basin
Lower San Joaquin River, CA
FINAL
Integrated Interim Feasibility Report/
Environmental Impact Statement/
Environmental Impact Report

ATTACHMENT D

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ATTACHMENT D

LOWER SAN JOAQUIN RIVER PROJECT INTERIM REPORT

SAN JOAQUIN COUNTY, CALIFORNIA

FINAL

INTEGRATED INTERIM FEASIBILITY REPORT/ENVIRONMENTAL IMPACT

STATEMENT/ENVIRONMENTAL IMPACT REPORT

JANUARY 2018

Type of Statement: Final Integrated Feasibility Report/Environmental Impact Statement/Environmental Impact Report (FR/EIS/EIR)

Lead NEPA Agency: U.S. Army Corps of Engineers, Sacramento District

Lead CEQA Agency: San Joaquin Area Flood Control Agency

Cooperating/Responsible Agency: State of California Central Valley Flood Protection Board

Abstract: The U.S. Army Corps of Engineers and its non- Federal sponsors, the San Joaquin Area Flood Control Agency and the State of California Central Valley Flood Protection Board, propose to improve flood risk management in North and Central Stockton by repairing and enhancing the levees that surround the city, and by constructing and operating closure structures on Fourteenmile Slough and Smith Canal .

The final FR/EIS/EIR describes the environmental resources in the project area; evaluates the direct, indirect, and cumulative environmental effects of the seven alternative plans, including the Recommended Plan (preferred alternative) ; and identifies avoidance, minimization, and compensatory mitigation measures. Most potential adverse effects would either be short term, or would be avoided or reduced using best management practices. However, there are some significant and unavoidable impacts associated with this project.

Public Review and Comment: The public review period for the draft FR/EIS/EIR began on February 27, 2015, and the official closing date for receipt of comments was April 13, 2015. All comments received were considered and incorporated into the final FS/EIS/EIR, as appropriate. The public review period for the final FR/EIS/EIR will begin when the notice of availability is published in the Federal Register on February 9, 2018, and will close 30 days later. Written comments or questions concerning this document should be directed to the following: Headquarters, U.S. Army Corps of Engineers, ATTN: CECW-P (IP), 7701 Telegraph Road, Alexandria, VA 22315-3860 or San Joaquin Area Flood Control Agency; Attn: Mr.

Juan Neira, 22 East Weber Avenue, Suite 301, Stockton, California 95202-2317, or by e mail at [email protected].

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REPORT CONTENTS

EXECUTIVE SUMMARY
CHAPTER 1 — STUDY INFORMATION
PURPOSE AND NEED FOR THE PROJECT AND REPORT .................................................................... 1-1 STUDY AUTHORITY .................................................................................................................................. 1-2 PROJECT LOCATION, STUDY AREA AND PROJECT AREA ............................................................... 1-5 STUDY SPONSORS AND PARTICIPANTS ............................................................................................... 1-8 HISTORY OF LOWER SAN JOAQUIN RIVER INVESTIGATIONS ....................................................... 1-8 EXISTING PROGRAMS, STUDIES AND PROJECTS............................................................................. 1-11 ENVIRONMENTAL REGULATORY FRAMEWORK ............................................................................ 1-16 REPORT ORGANIZATION ....................................................................................................................... 1-17 CHAPTER 2 — NEED AND OBJECTIVES FOR ACTION
PROBLEMS AND OPPORTUNITIES ......................................................................................................... 2-1 OBJECTIVES AND CONSTRAINTS .......................................................................................................... 2-8 INVENTORY AND FORECAST OF FUTURE WITHOUT PROJECT CONDITIONS........................... 2-10 CHAPTER 3 — PLAN FORMULATION
MEASURES .................................................................................................................................................. 3-1 FORMULATION AND EVALUATION OF INITIAL ALTERNATIVE PLANS ....................................... 3-4 INITIAL ALTERNATIVES ANALYSIS ...................................................................................................... 3-6 FOCUSED ARRAY OF ALTERNATIVES .................................................................................................. 3-7 COMPARISON OF FINAL ARRAY OF ALTERNATIVE PLANS AND DECISION CRITERIA ......... 3-18 EO 11988, FLOODPLAIN MANAGEMENT ............................................................................................. 3-28

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ENVIRONMENTAL CONSIDERATIONS AND MITIGATION ............................................................. 3-40 IDENTIFICATION OF THE NED PLAN .................................................................................................. 3-41 SELECTING A RECOMMENDED PLAN ................................................................................................. 3-44 THE RECOMMENDED PLAN .................................................................................................................. 3-46 CHAPTER 4 — DESCRIPTION OF FINAL ALTERNATIVES
INTRODUCTION.......................................................................................................................................... 4-1 ALTERNATIVES CONSIDERED IN DETAIL ........................................................................................... 4-2 FINAL PROPOSED STRUCTURAL MEASURES ..................................................................................... 4-2 ALTERNATIVES ........................................................................................................................................ 4-23

CONSTRUCTION DURATION AND CONSTRUCTION FOOTPRINT (I NCLUDING STAGING, BORROW AND DISPOSAL) ..................................................................................................................... 4-31 ESTABLISHMENT OF ETL COMPLIANT LEVEES ............................................................................... 4-37 CHAPTER 5 — AFFECTED ENVIRONMENT AND ENVIRONMENTAL CONSEQUENCES GEOLOGY AND GEOMORPHOLOGY ...................................................................................................... 5-3

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SEISMICITY ................................................................................................................................................. 5-6 SOILS AND MINERAL RESOURCES ...................................................................................................... 5-10 HYDROLOGY AND HYDRAULICS ........................................................................................................ 5-14 WATER QUALITY ..................................................................................................................................... 5-44 GROUNDWATER ...................................................................................................................................... 5-52 WETLANDS AND OTHER WATERS OF THE UNITED STATES ........................................................ 5-55

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AIR QUALITY AND GREENHOUSE GAS EMISSIONS ........................................................................ 5-67 VEGETATION .......................................................................................................................................... 5-107 WILDLIFE ................................................................................................................................................. 5-128 FISHERIES ................................................................................................................................................ 5-135 SPECIAL STATUS SPECIES ................................................................................................................... 5-144 Special Status Wildlife Species ................................................................................................. 5-152

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Special Status Plant Species ...................................................................................................... 5-159 Special Status Fish Species ....................................................................................................... 5-160 Special Status Wildlife Species ................................................................................................. 5-172 Special Status Fish Species ....................................................................................................... 5-173 Special Status Wildlife Species ................................................................................................. 5-174 Special Status Fish Species ....................................................................................................... 5-174 Special Status Wildlife Species ................................................................................................. 5-175 Special Status Plant Species ...................................................................................................... 5-178 Special Status Fish Species ....................................................................................................... 5-179 Special Status Wildlife Species ................................................................................................. 5-183 Special Status Plant Species ...................................................................................................... 5-184 Special Status Fish Species ....................................................................................................... 5-184 Special Status Wildlife Species ................................................................................................. 5-185 Special Status Plant Species ...................................................................................................... 5-185 Special Status Fish Species ....................................................................................................... 5-185 Special Status Wildlife Species ................................................................................................. 5-186 Special Status Plant Species ...................................................................................................... 5-186 Special Status Fish Species ....................................................................................................... 5-186 Special Status Wildlife Species ................................................................................................. 5-187 Special Status Plant Species ...................................................................................................... 5-187 Special Status Fish Species ....................................................................................................... 5-187 Special Status Wildlife Species ................................................................................................. 5-188 Special Status Plant Species ...................................................................................................... 5-188 Special Status Fish Species ....................................................................................................... 5-188 Special Status Wildlife Species ............................................................................................... 5-190 Special Status Plant Species .................................................................................................... 5-197 Special Status Fish Species ..................................................................................................... 5-198 SOCIOECONOMICS AND ENVIRONMENTAL JUSTICE ................................................................... 5-200 LAND USE ................................................................................................................................................ 5-209

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TRANSPORTATION ................................................................................................................................ 5-221 UTILITIES AND PUBLIC SERVICES .................................................................................................... 5-234 RECREATION .......................................................................................................................................... 5-242 AESTHETICS ............................................................................................................................................ 5-246 NOISE ........................................................................................................................................................ 5-251

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PUBLIC HEALTH AND ENVIRONMENTAL HAZARDS .................................................................... 5-263 CULTURAL RESOURCES ...................................................................................................................... 5-270 GROWTH INDUCEMENT ....................................................................................................................... 5-285 CUMULATIVE EFFECTS ........................................................................................................................ 5-286 UNAVOIDABLE SIGNIFICANT ENVIRONMENTAL EFFECTS ........................................................ 5-307 IRREVERSIBLE AND IRRETRIEVABLE COMMITMENT OF RESOURCES ................................... 5-309

RELATIONSHIP BETWEEN SHORT-TERM USES OF THE ENVIRONMENT AND LONG-TERM PRODUCTIVITY ...................................................................................................................................... 5-310 CHAPTER 6 — COORDINATION AND CONSULTATION
PUBLIC INVOLVEMENT UNDER NEPA AND CEQA ............................................................................ 6-1 COORDINATION WITH OTHER FEDERAL, STATE, REGIONAL AND LOCAL AGENCIES ............ 6-2 CONSULTATION WITH NATIVE AMERICAN TRIBES ......................................................................... 6-5 ISSUES OF KNOWN OR EXPECTED CONTROVERSY .......................................................................... 6-6

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CHAPTER 7 — COMPLIANCE WITH APPLICABLE LAWS, POLICIES AND PLANS FEDERAL REQUIREMENTS ...................................................................................................................... 7-1 STATE REQUIREMENTS............................................................................................................................ 7-9 LOCAL PLANS AND POLICIES ............................................................................................................... 7-16 CHAPTER 8 — RECOMMENDED PLAN
RECOMMENDED PLAN ............................................................................................................................. 8-1

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PLAN IMPLEMENTATION ....................................................................................................................... 8-19 SCHEDULE ................................................................................................................................................. 8-23 FURTHER STUDIES .................................................................................................................................. 8-24 CHAPTER 9 — RECOMMENDATIONS
CHAPTER 10 — LIST OF RECIPIENTS
ELECTED OFFICIALS AND REPRESENTATIVES ................................................................................ 10-1 FEDERAL GOVERNMENT AGENCIES .................................................................................................. 10-2 STATE OF CALIFORNIA GOVERNMENT AGENCIES ......................................................................... 10-3 REGIONAL, COUNTY, AND CITY AGENCIES ..................................................................................... 10-3 NATIVE AMERICAN TRIBES .................................................................................................................. 10-4 CHAPTER 11 — LIST OF PREPARERS
USACE......................................................................................................................................................... 11-1 ESA CONSULTING .................................................................................................................................... 11-4 CALIFORNIA DEPARTMENT OF WATER RESOURCES ..................................................................... 11-4 SJAFCA ....................................................................................................................................................... 11-5 PETERSON BRUSTAD ENGINEERING, INC. ........................................................................................ 11-5 CHAPTER 12 — REFERENCES
CHAPTER 13 — INDEX

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Tables
Table 1-1: Project Design Flood Flows ................................................................................................................... 1-13 Table 1-2: Reservoirs with Dedicated FRM Storage, San Joaquin River Basin ...................................................... 1-14 Table 1-3: Responsible and Trustee Agencies (CEQA) .......................................................................................... 1-17 Table 2-1: Structures Located within the 1/500 ACE Floodplain.............................................................................. 2-7 Table 2-2: Value of Damageable Property within the 1/500 ACE Floodplain ($1,000s) .......................................... 2-7 Table 3-1: Initial Screening of Management Measures ............................................................................................. 3-2 Table 3-2: Summary of Management Measures Retained or Dropped ...................................................................... 3-3 Table 3-3: Inclusion of Measures in Initial Alternative Plans ................................................................................... 3-5 Table 3-4: Initial Alternatives Retained ..................................................................................................................... 3-7 Table 3-5: Focused Array of Alternatives ................................................................................................................. 3-8 Table 3-6: Final Alternative Descriptions ............................................................................................................... 3-19 Table 3-7: Planning Criteria Analysis for Final Alternatives .................................................................................. 3-27 Table 3-8: LSJRFS Waterside Vegetation1 Directly Impacted by Implementation of Each Action Alternative ..... 3-41 Table 3-9: Economic Summary for Final Alternatives ............................................................................................ 3-41 Table 3-10: Residual Damages ................................................................................................................................ 3-42 Table 3-11: Comparison of Alternatives to Principles and Guidelines System of Accounts ................................... 3-44 Table 3-12: Comparison of Alternatives ................................................................................................................. 3-45 Table 4-1: Structural Measures Included in Each Action Alternative ....................................................................... 4-3 Table 4-2: Action Alternatives Measures by Waterway—North Stockton.............................................................. 4-24 Table 4-3: Action Alternatives Measures by Waterway— Central Stockton ........................................................... 4-24 Table 4-4: Action Alternatives Measures by Waterway— RD17 ............................................................................ 4-26 Table 4-5: Estimated Operations of the Mormon Channel Bypass Control Structure ............................................. 4-31 Table 4-6: Construction and Easement Footprints (Structural Features), Construction and O&M Easements and Construction Duration ............................................................................................................................ 4-32 Table 4-7: Estimated Borrow Material and Lands Required for Each Alternative .................................................. 4-34 Table 4-8: Total hours per month gate would have been closed assuming 2010 Sea Level Conditions. 1983 to 2014 ....................................................................................................................................................... 4-37 Table 5-1: Key to Effect Findings (by Increasing Adversity).................................................................................... 5-2 Table 5-2 Maximum Credible Earthquake Magnitudes ............................................................................................. 5-8 Table 5-3: Approximate Area of Disturbance by Alternative .................................................................................. 5-13 Table 5-4: Impacts to Waters of the U.S. ................................................................................................................ 5-60 Table 5-5: State and National Criteria Air Pollutant Standards, Effects and Sources ............................................. 5-69 Table 5-6: San Joaquin Valley Attainment Status ................................................................................................... 5-70 Table 5-7: Summary of Relevant California GHG Regulations .............................................................................. 5-74 Table 5-8: Air Quality Monitoring Data for San Joaquin County ........................................................................... 5-76 Table 5-9: Alternative 7a Annual Construction Emissions ..................................................................................... 5-84 Table 5-10: NOx Reductions from Implementation of Tier 3 Mitigation................................................................ 5-85 Table 5-11: Alternative 7a Mitigated NOx emissions ............................................................................................. 5-86 Table 5-12: Alternative 7a Construction NOx Mitigation Fee Calculation ............................................................. 5-86 Table 5-13: Alternative 7b Annual Construction Emissions ................................................................................... 5-89 Table 5-14: NOx Reductions from Implementation of Tier 3 Mitigation................................................................ 5-89 Table 5-15: Alternative 7b Mitigated NOx Emissions ............................................................................................ 5-90 Table 5-16: Alternative 7b Construction NOx Mitigation Fee Calculation ............................................................. 5-90 Table 5-17: Alternative 8a Annual Construction Emissions.................................................................................... 5-93 Table 5-18: NOx Reductions from Implementation of Tier 3 Mitigation................................................................ 5-93 Table 5-19: Alternative 8a Mitigated NOx emissions ............................................................................................. 5-94 Table 5-20: Alternative 8a Construction NOx Mitigation Fee Calculation ............................................................. 5-94 Table 5-21: Alternative 8b Annual Construction Emissions ................................................................................... 5-97 Table 5-22: NOx Reductions from Implementation of Tier 3 Mitigation................................................................ 5-97 Table 5-23: Alternative 8b Mitigated NOx Emissions ............................................................................................ 5-98 Table 5-24: Alternative 8b Construction NOx Mitigation Fee Calculation ............................................................. 5-98 Table 5-25: Alternative 9a Annual Construction Emissions.................................................................................. 5-101 Table 5-26: NOx Reductions from Implementation of Tier 3 Mitigation.............................................................. 5-101 Table 5-27: Alternative 9a Mitigated NOx Emissions........................................................................................... 5-102

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Table 5-28: Alternative 9a Construction NOx Mitigation Fee Calculation ........................................................... 5-102 Table 5-29: Alternative 9b Annual Construction Emissions ................................................................................. 5-105 Table 5-30: NOx Reductions from Implementation of Tier 3 Mitigation.............................................................. 5-105 Table 5-31: Alternative 9b Mitigated NOx Emissions .......................................................................................... 5-106 Table 5-32: Alternative 9b Construction NOx Mitigation Fee Calculation ........................................................... 5-106 Table 5-33: Vegetation Effects by Alternatives ..................................................................................................... 5-118 Table 5-34: Fish Species Reported in the Study Area ........................................................................................... 5-136 Table 5-35: Special Status Species and Critical Habitats ...................................................................................... 5-146 Table 5-36: Study Area Potential Elderberry Shrubs............................................................................................. 5-176 Table 5-37: Race/Origin Characteristics and Poverty Status by City/County/State, 2010 (Percent) ..................... 5-204 Table 5-38: Approximate Distances to UPRR Noise Contours ............................................................................. 5-252 Table 5-39: FTA Groundborne Vibration Impact Criteria for General Assessment .............................................. 5-254 Table 5-40: Exterior Noise Exposure Criteria Applied to Stationary Noise Sources at Residential Receivers ..... 5-255 Table 5-41: Typical Maximum Noise Level for Construction Equipment ............................................................ 5-257 Table 5-42: Predicted Noise Levels Due to Major Construction Activities for All Alternatives .......................... 5-257 Table 5-43: Typical Construction Equipment Vibration ....................................................................................... 5-258 Table 5-44: Recorded Cultural Resources within Alternative 7a (RP) .................................................................. 5-278 Table 5-45: Geographic Area That Would be Affected by the LSJR Project ........................................................ 5-288 Table 5-46: Development Projects within RD 17 .................................................................................................. 5-295 Table 5-47: Projects Requesting Section 408 Approval ........................................................................................ 5-299 Table 5-48: Significant and Unavoidable Environmental Impacts of the RP, Alternative 7a ............................... 5-308 Table 8-1: Environmental Commitments .................................................................................................................. 8-8 Table 8-2: Environmental Impacts and Compensatory Mitigation for the Recommended Plan ............................. 8-10 Table 8-3: Recommended Plan Lands, Easements and Rights-of-Way................................................................... 8-13 Table 8-4: Estimated Costs of Recommended Plan ($1,000) .................................................................................. 8-14 Table 8-5: Annual Costs and Benefits for Recommended Plan ($1,000) ................................................................ 8-14 Table 8-6: Summary of Cost Sharing Responsibilities for the Recommended Plan ($1,000s) ............................... 8-15 Table 8-7: Project Schedule ..................................................................................................................................... 8-23

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Figures
Figure 1-1: Study Authority Extent ........................................................................................................................... 1-4 Figure 1-2: Study Area .......................................................................................................................................... 1-6 Figure 1-3: Lower San Joaquin River Feasibility Study Area ............................................................................... 1-7 Figure 2-1: Topography of Lower San Joaquin River Floodplain ............................................................................. 2-2 Figure 2-2: 0.2% Median ACE Floodplain ................................................................................................................ 2-3 Figure 2-3: Peak Annual Flows from USGS Gage at Vernalis .................................................................................. 2-4 Figure 2-4: Flooding Looking West Across the South Stockton Area (1955) ........................................................... 2-5 Figure 2-5: Study Area Levees .................................................................................................................................. 2-6 Figure 3-1: Alternative 2a ........................................................................................................................................ 3- 11 Figure 3-2: Alternative 2b ....................................................................................................................................... 3- 12 Figure 3-3: Alternative 4 ......................................................................................................................................... 3- 13 Figure 3-4: Alternative 7 ......................................................................................................................................... 3- 14 Figure 3-5: Alternative 8 ......................................................................................................................................... 3- 15 Figure 3-6: Alternative 9 ......................................................................................................................................... 3- 16 Figure 3-7: Alternative 10 ....................................................................................................................................... 3- 17 Figure 3-8: Alternative 7a ........................................................................................................................................ 3- 20 Figure 3-9: Alternative 7b ....................................................................................................................................... 3- 21 Figure 3-10: Alternative 8a ...................................................................................................................................... 3- 22 Figure 3-11: Alternative 8b ..................................................................................................................................... 3- 23 Figure 3-12: Alternative 9a ...................................................................................................................................... 3- 24 Figure 3-13: Alternative 9b ..................................................................................................................................... 3- 25 Figure 3-14: Decision Making Process for EO 11988 ............................................................................................. 3- 28 Figure 3-15: San Joaquin River East Levee System ................................................................................................ 3- 32 Figure 3-16: Existing Land Use in Study Area ........................................................................................................ 3- 36 Figure 3-17: Planned Development RD 17 and 1% ACE Inundation Area ............................................................. 3- 37 Figure 3-18: North Stockton Residual Risk ............................................................................................................. 3- 43 Figure 3-19: Central Stockton Residual Risk .......................................................................................................... 3- 43 Figure 4-1: Cutoff Wall Typical Plan ........................................................................................................................ 4-7 Figure 4-2: Levee Reshaping and Levee Raise Typical Plan .................................................................................... 4-9 Figure 4-3: Seepage Berm Typical Plan .................................................................................................................. 4- 12 Figure 4-4: New Levee with Cutoff Wall Typical Plan ........................................................................................... 4- 13 Figure 4-5: Seismic Remediation Typical Plan ....................................................................................................... 4- 17 Figure 4-6: Mormon Channel Bypass Control Structure ......................................................................................... 4- 21 Figure 5-1: The Delta .............................................................................................................................................. 5- 16 Figure 5-2: 1997 Flood Wetherbee Lake and RD17 Tieback Levee ....................................................................... 5- 19 Figure 5-3: Calaveras River Watershed Boundary .................................................................................................. 5- 22 Figure 5-4: Bear Creek Watershed Boundary .......................................................................................................... 5- 23 Figure 5-5: French Camp Slough Watershed Boundary .......................................................................................... 5- 25 Figure 5-6: Mosher Slough Watershed Boundary ................................................................................................... 5- 26 Figure 5-7: Natural Composite Floodplain— Alternative 1 (No Action Plan) ......................................................... 5-28 Figure 5-8: R&U Composite Floodplain—Alternative 1 (No Action Plan) ............................................................ 5- 29 Figure 5-9: R&U Composite Floodplain—Alternative 7a ....................................................................................... 5- 33 Figure 5-10: R&U Composite Floodplain— Alternative 7b .................................................................................... 5- 35 Figure 5-11: R&U Composite Floodplain— Alternative 8a ..................................................................................... 5- 37 Figure 5-12: R&U Composite Floodplain— Alternative 8b .................................................................................... 5- 39 Figure 5-13: R&U Composite Floodplain— Alternative 9a ..................................................................................... 5- 41 Figure 5-14: R&U Composite Floodplain— Alternative 9b .................................................................................... 5- 43 Figure 5-15: 2035 General Plan Land Use/Circulation Diagram........................................................................... 5- 208 Figure 5-16: Stockton Planning Boundaries .......................................................................................................... 5- 212 Figure 5-17: Williamson Act Contracts in the Study Area .................................................................................... 5- 214 Figure 5-18: Transportation Routes ....................................................................................................................... 5- 223 Figure 5-19: Residential Levee with Waterfront Views (Fourteenmile Slough) ................................................... 5-247 Figure 5-20: Old Mormon Slough ......................................................................................................................... 5- 248 Figure 5-21: Noise Impact Criteria for Transit Projects (FTA 2006) .................................................................... 5- 253

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Figure 8-1: Recommended Plan and Design Feature ................................................................................................ 8-4 Figure 8-2: Existing Federal, non-Federal becoming Federal and New Levees ........................................................ 8-5 Appendices
APPENDIX A: ECONOMICS

APPENDIX B: ENGINEERING
APPENDIX C: REAL ESTATE

Study Addenda*
A. ECONOMICS ADDENDA
B. ENGINEERING ADDENDA
C. REAL ESTATE ADDENDA
D. ENVIRONMENTAL ADDENDA
E. GEOTECHNICAL ADDENDA
F. HYDRAULICS ADDENDA
G. HYDROLOGY ADDENDA
H. COST ENGINEERING ADDENDA
I. PLAN FORMULATION ADDENDA

*All documents can be found on http://www.spk.usace.army.mil/lower_sj_river

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LIST OF ACRONYMS
AADT Annual Average Daily Traffic
AB Assembly Bill
ACE Annual Chance of Exceedance
AEP Annual Exceedance Probability
ATR Agency Technical Review
BA Biological Assessment
BDCP Bay Delta Conservation Plan
BMP(s) Best Management Practice(s)
BNSF Burlington Northern Santa Fe Railroad
BO Biological Opinion
BSC Building Standards Commission
BSSCP Bentonite Slurry Spill Contingency Plan
CAA Clean Air Act
CAR Coordination Act Report
CARB California Air Resources Board
CCR California Code of Regulations
CCT Central California Traction Company
CDC California Department of Conservation
CDFG California Department of Fish and Game
CDFW California Department of Fish and Wildlife
CEQ Council on Environmental Quality
CEQA California Environmental Quality Act
CERCLA Comprehensive Environmental Response, Compensation, and Liability Act CFGC California Fish and Game Code
CFR Code of Federal Regulations
cfs cubic feet per second
CH4 Methane
CLD California Levee Database
CLSP Central Lathrop Specific Plan
CMP Congestion Management Program
CNDDB California Natural Diversity Database
CNPS California Native Plant Society
CO2 Carbon dioxide
CO2e Carbon dioxide equivalent
CRHR California Register of Historical Resources
CVFPB Central Valley Flood Protection Board
CVFPP Central Valley Flood Protection Plan
CVP Central Valley Project
CVPIA Central Valley Project Improvement Act
CWA Clean Water Act
cy cubic yards
dB decibel
dBA Weighted decibel
DDT dichlorodiphenyltrichloroethane
DEIS/DEIR Draft Environmental Impact Statement/Draft Environmental Impact Report Delta Sacramento-San Joaquin Delta
DO dissolved oxygen
DPM Diesel Particulate Matter
DPS Distinct Population Segment
DSC Delta Stewardship Council
DSM DEEP Soil Mixing

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DTSC Department of Toxic Substances Control
DWR Department of Water Resources
DWSC Deep Water Ship Channel
DWSP Delta Water Supply Project
EO Executive Order
EC electrical conductivity
EC Engineer Circular
EFH Essential Fish Habitat
EMT Emergency Medical Trained
EOPs Environmental Operating Principles
EQ Environmental Equality
ER Ecosystem Restoration
ESA Endangered Species Act
ESU Evolutionarily Significant Unit
ETL Engineer Technical Letter
FCSA Feasibility Cost Sharing Agreement
FEMA Federal Emergency Management Agency
FPPA Farmland Protection Policy Act
FR Federal Register
FR/EIS/EIR Feasibility Report/Environmental Impact Statement/Environmental Impact Report FRM Flood Risk Management
FSZ Farmland Security Zone
ft feet
FTA Federal Transit Administration
FWCA Fish and Wildlife Coordination Act
FWEEP Flood Warning, Emergency Evacuation Plan
FWOP Future Without Project
GCR General Conformity Rule
GGS Giant Garter Snake
GHG Greenhouse Gas
gpm gallons per minute
GWP Global Warming Potential
HABS Historic American Building Survey
HFCs Hydrofluorocarbons
HFEs Hydrofluorinated ethers
HPTPs Historic Property Treatment Plans
HTRW Hazardous, Toxic and Radioactive Waste
IEPR Independent External Peer Review
LAFCO Local Agency Formation Commission
Ldn level of day-night sound
LERRDs Lands, Easements, Rights of Way, Relocations, and Disposal Sites LESA Land Evaluation and Site Assessment
lf Linear Feet
LOS Level of Service
LPP Locally Preferred Plan
LSAP Levee Seepage Area Project
LSJR Lower San Joaquin River
LSJRFS Lower San Joaquin River Feasibility Study
MBTA Migratory Bird Treaty Act
MCACES Micro Computer-Aided Cost Engineering System
MCL Maximum Contaminant Levels
mgd million gallons per day
N2O Nitrous oxide

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NAAQS National Ambient Air Quality Standards
NAD 83 North American Horizontal Datum of 1983
NED National Economic Development
NEPA National Environmental Policy Act
NF3 Nitrogen trifluoride
NFIP National Flood Insurance Program
NFS non-Federal Sponsors
NH4 ammonium
NHPA National Historic Preservation Act
NLD National Levee Database
NMFS National Marine Fisheries Service
NO2 nitrite
NO3 nitrate
NOI Notice of Intent
NOP Notice of Preparation
NOx Nitrogen oxides
NPDES National Pollutant Discharge Elimination System
NRCS Natural Resources Conservation Service
NRHP National Register of Historic Places
NSAS-HD Naval Supply Annex Stockton Historic District
NULE Non-Urban Levee Evaluation
NWI National Wetland Inventory
O&M Operations and Maintenance
OEHHA Office of Environmental Health Hazard Assessment
OMRR&R Operation, Maintenance, Repair, Replacement and Rehabilitation OPR Office of Planning and Research
OSE Other Social Effects or Social Wellbeing
PA Programmatic Agreement
PCBs polychlorinated biphenyls
PCET Parametric Cost Estimation Tool
PED Preconstruction Engineering and Design
PFCs perfluorocarbons
PL Public Law
PM10 Respirable Particulate Matter
PM2.5 Fine Particulate Matter
PPA Project Partnership Agreement
ppm Parts per Million
ppt Parts per thousand
PRC Public Resource Code
R&U Risk and Uncertainty
RCEM Road Construction Emission Model
RDEIR/SDEIS Recirculated Draft Environmental Impact Report/Supplemental Draft Environmental Impact Statement
RED Regional Economic Development
rkm River kilometer
ROG Reactive organic gases
RP Recommended Plan
RWCF Regional Wastewater Control Facility
RWQCB Regional Water Quality Control Board
SB 5 Senate Bill 5
SDC Stockton Diverting Canal
SEWD Stockton East Water District
SF6 Sulfur hexafluoride

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SHPO State Historic Preservation Office
SIPs State Implementation Plans
SJAFCA San Joaquin Area Flood Control Agency
SJCOG San Joaquin Council of Governments
SJMSCP San Joaquin County Multi-Species Habitat Conservation and Open Space Plan SJR San Joaquin River
SJVAB San Joaquin Valley Air Basin
SJVAPCD San Joaquin Valley Air Pollution Control District SLC Sea Level Change
SMARA Surface Mining and Reclamation Act
SMGB State Mining and Geology Board
SOI Sphere of Influence
SPCCP Spill Prevention, Control and Counter Measure Plan SPD South Pacific Division
SPFC State Plan of Flood Control
SPRR Southern Pacific Railroad
sq ft Square feet
SRA Shaded Riverine Aquatic
STE Stockton Terminal and Eastern Railroad
SWPPP Stormwater Pollution Prevention Plan
SWRCB State Water Resources Control Board
TAC Toxic Air Contaminants
TDS Total Dissolved Solids
TMDL Total Maximum Daily Load
TSP Tentatively Selected Plan
TWAE Temporary Work Area Easements
ULDC Urban Levee Design Criteria
ULE Urban Levee Evaluation
ULOP Urban Level of Protection
UPRR Union Pacific Railroad
USACE U.S. Army Corps of Engineers
USBR United States Bureau of Reclamation
USC U.S. Code
USCB U.S. Census Bureau
USEPA U.S. Environmental Protection Agency
USFWS U.S. Fish and Wildlife Service
VdB Vibration decibels
VELB valley elderberry longhorn beetle
VERA Verified Emission Reduction Agreement
VFZ Vegetation Free Zone
WRDA Water Resources Development Act

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EXECUTIVE SUMMARY

INTRODUCTION AND PURPOSE
The purpose of the Lower San Joaquin River Feasibility Study is to identify a cost-effective plan to reduce flood risk in the Stockton metropolitan area. An unacceptably high risk of flooding from le vee failure threatens the safety of 235,000 people, as well as property and critical infrastructure throughout the area.

This integrated Interim Feasibility Report and joint Environmental Impact Statement/Environmental Impact Report (FR/EIS/EIR) describes the planning process followed to develop and evaluate an array of alternatives and identify the Recommended Plan ( RP), which is also the Preferred Alternative under the National Environmental Policy Act (NEPA), to address flood risk management problems and opportunities in the Lower San Joaquin River (LSJR) basin. The RP identified in this study is also the Environmentally Preferable Alternative under NEPA and the Least Environmentally Damaging Practicable Alternative under the Clean Water Act. The U.S. Army Corps of Engineers, Sacramento District (USACE), the San Joaquin Area Flood Control Agency (SJAFCA), the State of California, represented by the Central Valley Flood Protection Board (CVFPB) and the Department of Water Resources (DWR) are sponsoring this study. This FR/EIS/EIR meets the environmental impact assessment and disclosure requirements of NEPA and the California Environmental Quality Act (CEQA). USACE is the lead agency under NEPA. SJAFCA is the lead agency under CEQA. CVFPB and DWR are cooperating agencies under NEPA and Responsible Agencies under CEQA.

The Draft FR/EIS/EIR was released for concurrent public review, internal policy review, Agency Technical Review (ATR) and Independent External Peer Review (IEPR). All comments received during the ATR, IEPR and the 45-day public review period were considered and incorporated into the Final FR/EIS/EIR, as appropriate. The Final FR/EIS/EIR presents the RP for potential authorization by Congress.

STUDY AREA
The LSJR Study area (Figure ES-1) is located along the northern portion of the San Joaquin River system in the Central Valley of California. The San Joaquin River originates on the western slope of the Sierra Nevada and emerges from the foothills at Friant Dam. The river flows west to the Central Valley, where it is joined by the Fresno, Chowchilla, Merced, Tuolumne, Stanislaus and Calaveras Rivers, and joined by smaller tributaries as it flows north to the Sacramento-San Joaquin Delta (Delta).

The overall study area, as defined in the study authorization, includes the mainstem of the San Joaquin River from the Mariposa Bypass downstream to the city of Stockton. The study area also includes the distributary channels of the San Joaquin River in the southernmost reaches of the Delta; Paradise Cut and Old River as far north as Tracy Boulevard, and Middle River as far north as Victoria Canal. Based on availability of potential non_Federal sponsors (NFS), the refined study area focused on approximately 305 square miles encompassing incorporated areas of Stockton, Lathrop and Manteca, as well as unincorporated portions of San Joaquin County. During the plan formulation process, approximately 15,000 acres of urban, urbanizing and agricultural lands were screened out due to lack of Federal interest. The screening was consistent with Executive Order 11988, Floodplain Management . The remaining study area was divided into three separable elements considered to be hydraulically separate, meaning that each area could have stand-alone solutions or alternatives proposed.

This study will only partially address the Sacramento – San Joaquin Basin Streams, California Comprehensive Study authority. Therefore, the Lower San Joaquin Feasibility Study (LSJRFS) report will be called an “Interim Feasibility Report”, which indicates that the study is addressing the flood risk issues of a specific area within the authority, rather than the entire area authorized for study. This does not rule out additional studies for this or other areas within the authorized study area at a future date.

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BACKGROUND AND NEED
Study Authority
The general authority for flood control investigations in the San Joaquin River Basin arises under the Flood Control Act of 1936 (Public Law [PL] 74-738), Sections 2 and 6, and amended by the Flood Control Act of 1938 (PL 75-761). Further studies of this river system were requested in the May 8, 1964 resolution adopted by the Committee on Public Works of the House of Representatives.

Study Background
USACE initiated the Feasibility Study in 2009 at the request of SJAFCA, the NFS for the study , through the execution of a Feasibility Cost Sharing Agreement (FCSA). CVFPB also entered the study as a signatory of the FCSA in 2010.

The study area has a history of flood events, with major floods occurring in 1955, 1958, and 1997. The 1955 event had the highest flows recorded on the Calaveras River at Bellota, and approximately 1,500 acres of Stockton were inundated to depths of 6 feet for as long as 8 days. The 1958 event inundated approximately 8,500 acres between Bellota and the Diverting Canal, with flood waters up to 2 feet deep and inundation durations from 2 to 10 days. The 1955 and 1958 floods occurred prior to completion of New Hogan Dam and Reservoir and improvements to the Calaveras River and Stockton Diverting Canal. The 1997 event resulted in the evacuation of the Weston Ranch area of Stockton at the north end of Reclamation District 17 (RD 17). While the 1997 event did not directly damage areas of Stockton, Lathrop or Manteca, there were approximately 1,842 residences and businesses affected in San Joaquin County. There were also significant flood-fighting efforts conducted during the 1997 event in RDs 404 and 17. Between the 2 RDs, flood-fights were required at 37 sites. Of interest to this study were breaches upstream of RD 17 along the San Joaquin and Stanislaus Rivers, resulting in the non- Federal tieback levee being highly stressed, but preventing flooding of urban areas in RD 17 and potentially central Stockton. Estimated damages in San Joaquin County for the 1997 event were approximately $80 million.

Analysis of the study area is challenged by the presence of three sources of flooding, the Delta Front, Calaveras River and San Joaquin River. This results in commingled floodplains for the North and Central Stockton areas. The distributary nature of the Delta also affects Delta water levels, because high flows from the Sacramento River may “fill” the Delta prior to a peak inflow on the San Joaquin River as occurred in 1997, raising water levels on the Delta front levees.

The existing levee system within the project area provides flood risk management (FRM) benefits to over 71,000 acres of mixed-use land with a current population estimated at 235,000 residents and an estimated $28.7 billion in damageable property. Further, as the floodplain habitat was altered, native functional habitats were lost, causing impacts to endangered and threatened species. In addition, the levees along the San Joaquin River effectively cut off direct public access to the river and its associated environmental and recreational amenities in many areas.

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The problems and opportunities in the Stockton area include:

Problem:
 There is significant risk to public health, safety and property in the study area associated with flooding.

Opportunities:
 Improve FRM in the study area.
 Sustain and improve aquatic, r iparian and adjacent terrestrial habitats in conjunction with FRM features.
 Integrate with other Federal, State and local initiatives.  Educate the public about residual flood risk.

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Note: AOI is an acronym for “Area of Interest”
Figure ES-1: The LSJR Study Area

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CONSIDERATION OF ALTERNATIVE PLANS
During the feasibility study, the Federal planning process for development of water resource projects was followed to identify a RP for recommendation to Congress. Following definition of flood related problems and opportunities, specific planning objectives and planning constraints were identified. Various management measures were identified to achieve the planni ng objectives and avoid constraints.

Management measures were combined to form an array of FRM alternative plans, which were developed on the basis of the north and central Stockton, and RD 17 areas being hydraulically separable.

The strategy to move the initial array of alternatives forward to a focused array of alternatives included the following steps: (1) apply metrics to evaluate alternative arrays; (2) select the best alternative for each separable area or levee reach based o n a parametric cost and benefit analysis; and (3) combine the best alternatives to be carried forward to the focused array. After additional analysis of the focused array of alternatives, it was determined that addressing potential sea level change during the period of analysis was economically justified and provided improved performance. This resulted in removing three alternatives from further consideration. The Final alternative plans were then compared to identify the plan that reasonably maximized net National Economic Development (NED) benefits consistent with protecting the Nation’s environment. The NED plan is also the RP.

ALTERNATIVES
The alter natives described in the Draft FR/EIS/EIR are discuss ed below. More information about the alternatives eliminated from consideration can be found in Chapter 3, Section 3.3.

Alternative 1, No Action. Under the No Action Alternative, USACE would not conduct any additional work to address seepage, slope stability, overtopping, or erosion concerns in the Stockton metropolitan area and RD 17. As a result, if a flood event were to occur, the Cities of Stockton, Lathrop, and Manteca, and surrounding agricultural and open space lands, would remain at risk of a possible levee failure and flooding.

In addition, the associated risk to human health and safety, property, and the adverse economic impact that serious flooding could cause would continue, and the risk of a catastrophic flood would remain high.

Regular operations and maintenance of the levee system would continue as presently executed by the local maintaining entities.

Alternative 7a, North and Central Stockton, Delta Front, Lower Calaveras River, and San Joaquin River Levee Improvements excluding RD 17. This alternative would implement levee improvements around North and Central Stockton and two closure structures; one on Fourteenmile Slough and one on Smith Canal. The alternative would combine the levee improvement measures of cutoff wall, deep soil mixing (seismic), and levee geometry improvements, and would address projected sea level change by including raising the levee height where needed. There is an additional levee extension on Duck Creek to prevent flanking.

Alternative 7b, North and Central Stockton, Delta Front, Lower Calaveras River, and San Joaquin River Levee Improvements including RD 17. This alternative would implement the same levee improvements and closure structures as Alternative 7a, but would also implement levee improvements and about 2.2 miles of new levees at the Old River flow split and a tie- back levee in RD 17. The new levees would include a cutoff wall to address potential seepage issues.

Alternative 8a, North and Central Stockton, Delta Front, Lower Calaveras River, San Joaquin River, and Stockton Diverting Canal Levee Improvements excluding RD 17. This alternative would implement levee improvements and two closure st ructures in North and Central Stockton. The alternative would combine the levee improvement measures of cutoff wall, deep soil mixing (seismic), and levee geometry improvements, and would address projected sea level change by including raises in levee height where needed. There is an additional levee extension on Duck Creek to prevent flanking.

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Alternative 8b, North and Central Stockton, Delta Front, Lower Calaveras River, San Joaquin River, and Stockton Diverting Canal Levee Improvements including RD 17. This alternative would implement levee improvements without including the Mormon Channel bypass. The alternative would combine the levee improvement measures of cutoff wall, deep soil mixing (seismic), seepage berm, and levee geometry improvements, and would address projected sea level change by including raising the levee height where needed. There would also be approximately 2.2 miles of new levee constructed to extend the RD 17 tie- back levee and the secondary levee at the Old River flow split. The new levees would include a cutoff wall to address potential seepage issues.

The difference in extent between Alternatives 7a , 7b and Alternatives 8a, 8b is the addition of reaches on the Calaveras River and the Stockton Diverting Canal left bank levee. The extra length of the reaches in Alternatives 8a, 8b totals approximately 55,500 feet (10.5 miles) of levee.

Alternative 9a, North and Central Stockton, Delta Front, Lower Calaveras River, San Joaquin River Levee Improvements and Mormon Channel Bypass excluding RD 17 . This alternative would implement levee improvements, as well as channel improvements within the Mormon Channel Bypass to increase capacity, and create a diversion control structure on the Stockton Diverting Canal that would restore flood flows to the Mormon Channel. The alternative would combine the levee improvement measures of cutoff wall, deep soil mixing (seismic), and levee geometry improvements, and would address projected sea level change by including raising the levee height where needed. There is an additional levee extension on Duck Creek to prevent flanking. The diversion control structure at the Stockton Diverting Canal would consist of pipe culverts with gates that control releases to a maximum flow of approximately 1,200 cubic feet per second (cfs). Constructing the improvements to the Mormon Channel would require removal of much of the existing vegetation, yet the restoration of flood flows to the Mormon Channel would provide multiple benefits, which is a priority for the NFS. These benefits could include establi shment of native vegetation, improved wetlands, and opportunities for passive recreation.

Alternative 9b, North and Central Stockton, Delta Front, Lower Calaveras River, San Joaquin River Levee Improvements and Mor mon Channel Bypass including RD 17 . This alternative would implement levee improvements along with restoration of the Mormon Channel, including a diversion control structure at the Stockton Diverting Canal. The alternative would combine the levee improvement measures of cutoff wall, deep soil mixing (seismic), seepage berm, and levee geometry improvements, and would address projected sea level change by including raising the levee height where needed. There would also be approximately

2.2 miles of new levee constructed to extend the RD17 tie- back levee and the secondary levee at the Old River flow split. The new levees would include a cutoff wall to address potential seepage issues. The diversion control structure at the Stockton Diverting Canal would consist of pipe culverts with gates that control releases to a maximum flow of approximately 1,200 cfs. The restoration of flood flows to the Mormon Channel would serve multiple public needs, including flood risk reduction, habitat restoration, and recreation, which are priorities of the NFS.

Alternatives 9a and 9b differ from Alternatives 7a and 7b by the addition of 33,400 feet (6.3 miles) of improvements along Mormon Channel, and inclusion of a diversion structure to divert flows from the Stockton Diverting Canal into Mormon Channel.

Mormon Slough’s course extends in a general southwesterly direction from Bellota to the Stockton Diverting Canal flow diversion structure. The structure diverts all flood flows to the diverting canal, which discharges into the Calaveras River. The Mormon Slough below the diverting dam is referred to locally as Mormon Channel. The source of flow in Mormon Channel is the local tributary area downstream of the diversion structure.

Before construction of the Stockton Diverting Canal, Mormon Channel was connected to Mormon Slough and was perennial in m ost years. Today, the channel receives local storm water runoff and intermittently contains water.

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Reintroducing flood flows to Mormon Channel by establishing the Mormon Slough Bypass would involve construction of a diversion structure at the confluence of Old Mormon Slough with the Stockton Diverting Canal, and excavation within Mormon Channel in order to establish the channel as Mormon Slough Bypass.

This would likely improve conditions for the remaining vegetation and would likely increase the health and encourage expansion of riparian vegetation along much of this channel.

AFFECTED ENVIRONMENT, ENVIRONMENTAL CONSEQUENCES, AND MITIGATION Initial evaluation of project effects indicated that there would likely be little to no effect on current geology and geomorphology, seismicity, soils and mineral resources, hydrology and hydraulics, and public health and environmental hazards. An evaluation of environmental effects determined that each of the final alternatives, including the RP, has the potential for adverse effects on air quality and greenhouse gasses, water quality, groundwater, wetlands and waters of the U.S., vegetation, wildlife, special status species , fisheries, aesthetics, recreation, transportation, noise, cultural re sources, utilities and public services , and land use, and socioeconomics. A comparison of environmental effects by alternative is provided in Table ES-1. The majority of the resource categories have a similar range of effects with the implementation of any of action alternatives.

Alternatives 7a, 8a and 9a differ from Alternatives 7b, 8b and 9b, respectively, in that the “b” alternatives all include levee improvements and new levee sections in RD 17. No work in RD 17 is proposed in any of the “a” alternatives. Each alternative proposes exactly the same improvements in North Stockton. Each pair of alternatives —7a and 7b, 8a and 8b, 9a and 9b — propose the same improvements in Central Stockton except that the “a” alternatives include a small additional levee extension on Duck Creek not included in the “b” alternatives. The differences among these alternatives are highlighted in Table ES-1.

Table ES-1: Differences Among the Action Alternatives
Alternatives
7a 7b 8a 8b 9a 9b
Additional levee improvements on Lower Calaveras River X X Levee Improvements on Stockton Diverting Canal X X
Flood Bypass through Old Mormon Channel X X
Levee extension on Duck Creek X X X
RD17 levee improvements and new levee segments X X X Because of the great extent of the proposed levee improvements and new levee segments, all of the “b” alternatives would have more effects than the “a” alternatives on vegetation, wildlife, fish, special status species, noise, air quality, aesthetics, recreation, and growth. Alternative 7a is the smallest alternative and has the least environmental impact. Alternatives 8b and 9b would have the greatest potential effects on vegetation, wildlife, fish, special status species, noise, air quality, aesthetics, and recreation. Alternatives 9a and 9b would restore flood flows to Old Mormon Channel and create opportunities for future restoration of riparian and wetlands habitat, yet the excavation required to establish the flood bypass would have greater potential impacts on air quality and transportation than the other alternatives. In comparison with Alternatives 7a and 9a, Alternative 8a would result in potential impacts to noise, recreation, and air quality as a result of the additional levee improvements on the Lower Calaveras River and the Stockton Diverting Canal.

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Construction of the flood risk management features for the RP would detrimentally affect fish and wildlife habitat. It would cause permanent losses of riparian habitat from construction activities required for excavations, floodwalls, levees, and Vegetation ETL compliance, affecting 139 acres of native riparian habitat. The RP would remove about 19,630 LF of shaded riverine aquatic habitat. The RP would remove approximately 10.75 acres of existing wetland habit at primarily associated with ditch fill and relocation.

An in-channel closure structure on Smith Canal and another on Fourteenmile Slough would temporarily affect 4 acres of open water, and 234 acres of shallow water habitat. Forty-one elderberry shrubs within the construction footprint would be transplanted to an on- site conservation area. The RP would permanently impact 12.5 acres of upland and 0.5 acres of aquatic giant garter snake (GGS) habitat. It w ould also temporarily impact 111.5 acres of upland and 6 acres of aquatic GGS habitat.

Some adverse environmental effects would be reduced to a less than significant level through project design, construction practices, preconstruction surveys and analysis , regulatory requirements, and best management practices. Compensatory mitigation would be required to reduce some impacts to less than significant. Even with compensatory mitigation, impacts would remain significant and unavoidable for the vegetation, wil dlife, fisheries, special status species, recreation , aesthetics, transportation, noise, and cultural resources.

COMPLIANCE WITH APPLICABLE LAWS, REGULATIONS, POLICIES AND PLANS This document is a joint EIS/EIR, and will fully comply with NEPA and CEQA requirements. The project will comply with all Federal and State laws, regulations, Executive Orders, and permit requirements.

PUBLIC INVOLVEMENT
Public involvement activities associated with the project included public meetings, Native American Tribe and agency meetings, and distribution of the Draft FR/EIS/EIR for public review and comment. On January 15, 2010, USACE published the Notice of Intent (NOI) to prepare a joint EIS/EIR for the LSJRFS in the Federal Register (Vol. 75, No. 10) and SJAFCA published a Notice of Preparation (NOP) with the State Clearinghouse (SCH # 2010012027). One public meeting was held on January 27, 2010 at the University of the Pacific in Stockton to initiate scoping on the FR/EIS/EIR while gathering additional information and community comments from citizens who live, work and commute near the project area. The public was invited to submit written comments during and after the meeting.

The Draft FR/EIS/EIR was circulated for a 45 -day review to Federal, State, and local agencies, organizations, and individuals who had previously expressed an int erest in the project. Public notification of the availability of the draft document for comment was published in the Federal Register and in local newspapers, posted to the Sacramento District website, electronically mailed to interested parties, and directly mailed to owners and occupants of property adjoining the parcel or parcels on which the project is located (CEQA Guidelines Section 15087) . A public workshop was held during the review period to provide additional opportunity for comments on the Draft FR/EIS/EIR. All comments received during the public review period have been considered and incorporated into the Final FR/EIS/EIR, as appropriate.

Comments and responses are included in the Environmental Addendum.

COMMUNICATION WITH NATIVE AMERICANS
Coordination with Native Americans included letters to the Ione Band of Miwok Indians, the Buena Vista Rancheria of Me- Wuk Indians, the Wilton Rancheria, the Notomne/Northern Valley Yokuts, and the California Valley Miwok Tribe in 2013. A draft PA was coordinated with the Tribes between 2013 and 2016. The United Auburn Indian Community expressed interest in 2015 and ha s since been included in consultations.

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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 was signed by USACE and the State Historic Preservation Officer (SHPO) on May 11, 2016.

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SIGNIFICANT ISSUES
Significant issues identified by agencies and the public related to construction of the LSJR Project are summarized below. These issues are based on preliminary studies and comments from formal and informal agency meetings, the public scoping meeting, and telephone conversations, letters, and emails.  Preliminary air quality emission calculations indicate that construction would result in air emissions that could lead to violations of applicable State ambient air quality standards and not comply with the Federal Clean Air Act (CAA). Concurrent construction activity could contribute additional emissions that would cumulatively fail to meet the general conformity rule of the CAA. Air quality impacts would be mitigated to less than significant in one of the following ways. (1) Require the use of off -road equipment that meets or exceeds USEPA or California Air Resources Board (CARB) Tier 3 off -road emission standards for all off-road vehicle greater than 25 horsepower and operating for more than 20 total hours over the entire duration of construction activities. Prior to issuance of a construction permit, the prime contractor would be required to prepare and submit a Construction Emissions Minimization Plan for review and approval. The plan would include estimates of the construction timeline by phase with a description of each piece of equipment required for every construction phase. (2) Implement a Verified Emission Reduction Agreement which would require payment of a fee to San Joaquin County Air Pollution Control District that would be used to purchase NOx emission reductions to offset all NOx emissions during the years when the Project’s unmitigated NOx emissions exceed 10 tons.  Construction of the project would require the permanent acquisition of private property within or near the construction area. Relocation of people, homes and businesses would be minimized to the extent feasible and consistent with the project purpose. Necessary rel ocations would be compensated under the Federal Relocation Act.
 Construction is expected to increase noise levels, affecting adjacent residents and local recreationists even under compliance with noise ordinances. Mitigation measures would be implemented to reduce impacts to the extent feasible. These measures are discussed in Chapter 5, section 5.19.10.  Noise, visual aesthetics, and access would be compromised during construction. Mitigation measures would be implemented to reduce impacts on noise (see sect ion 5.19.105.17.9), aesthetics (see section

5.18.10) and access (see section 5.17) Detours and alternative recreation locations would provide sufficient recreation opportunities in the study areas.  Construction would include compliance with the USACE Engineer Technical Letter (ETL) 1110 -2- 583. The removal of vegetation on levees would result in significant impacts to biological resources in the project area. The impact analysis assumes that on the waterside, up to 50 percent of the native trees and shrubs on the lower slope and within the 15 foot O&M easement may be allowed to remain through a variance to the ETL. For the purposes of Federal Endangered Species Act (ESA) Section 7 consultation 25 percent of the native trees and shrubs were assumed to remain on the lower waterside slope and within the waterside easement. If the RP is authorized, rigorous engineering studies would be conducted during PED to determine the suitability of the levees for a variance.  Construction of closure structures on Fourteenmile Slough and Smith Canal could result in take, as defined by the ESA, of special status fish species. The National Marine Fisheries Service and U.S. Fish and Wildlife Service issued biological opinions with incidental take statements in June 2016.  The overall project would be a multi-phased effort that may require overlapping construction activities within the overall p roject area. The timeline used in this analysis assumes work is sequential. If the project is authorized, additional project information would be developed during preconstruction engineering and design phase (PED). Any revisions to the construction timing and sequencing would be evaluated to determine if impacts have been fully addressed in this final FR/EIS/EIR or if a supplemental NEPA and/or subsequent CEQA document would be required.

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AREAS OF CONTROVERSY
NEPA requires identification of issues of known controversy that have been raised in the scoping process and throughout the development of the project. Potentially controversial issues that may arise discussed below.

Property Acquisition: A specific issue of concern involves potential conflicts with pr ivate property that is within or near the construction area. In some cases, permanent property acquisition may be needed for project construction, operation, and maintenance. Temporary construction easements may also be needed for construction staging and equipment access. These effects guide the Real Estate Plan and are generally described in Chapter 5, Section 5.14-
Land Use.

Construction Related Effects: The levee system in the project area is close to residential areas and other developed land uses. Therefore, actions proposed by the project are likely to resul t in construction related effects that may include noise, traffic, air quality, visual resources, and recreation, and are specifically described in Chapter 5 . A specific discussion about effects on residents is contained in Section

5.13,
Socioeconomics and Environmental Justice.

Levee Encroachments and Vegetation: The project alternatives include removal, relocation, or replacement of features in, on, or under the levee or adjacent operations and maintenance (O& M) corridors such as structures, pipelines, walls, stairs, utilities, and other elements such as vegetation, to comply with USACE ETL 1110-2-583. Implementation of such guidance has stirred controversy in the Central Valley as cursory assessments have shown that much vegetation may require removal, resulting in effects on fish and wildlife habitat, including habitat for endangered and threatened species. This may affect recreation and aesthetics.

This issue is described further in the effects discussions for vegetation, fish, wildlife, visual resources, and recreation in Chapter 5. Other encroachments are addressed in the land use and utilities sections of Chapter

5. Executive Order 11988 and Growth Inducement: Application of the Executive Order to this study has raised concerns about the ability of local jurisdictions to meet planning and development goals. These concerns are particularly relevant to the RD17 portion of the project area. The project’s potential to induce growth, or remove a potential barrier to growth, is discussed in Chapter 3, Section 3.6 and in Chapter 5, Section

5.22. SCOPE OF ENVIRONMENTAL ANALYSIS
The LSJRFS FR/EIS/EIR documents the Feasibility Study’s consideration of the level of Federal participation in FRM for the overall defined study area, including the Cities of Stockton, Lathrop, Manteca and surrounding urbanized areas. This Final FR/EIS/EIR analyzes the environmental effects of the proposed alternatives using a conservative approach that looks at typical cross sections and footprints for levee reaches. As planning proceeds, USACE, CVFPB and SJAFCA will continue to refine project elements, construction methods, equipment types and construction schedules with the intention of further reducing adverse impacts identified in Table ES-5, Chapter 4, and Chapter 5. Any refinements to project elements that occur during the PED or the construction phase will be reviewed and compared to what was evaluated in this FR/EIS/EIR to determine if supplemental NEPA and/or CEQA documentation will be required.

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San Joaquin County, CA Executive Summary

RECOMMENDED PLAN
The RP is Alternative 7a, North and Central Stockton – Delta Front, Lower Calaveras River and San Joaquin River Levee Improvements excluding RD 17 ( Figure ES-2). This plan meets the study objectives of reducing flood risk and flood damages. The RP greatly reduces flood risk to people and property in the city of Stockton, revitalizing local levees that were built to reduce the chance of hazardous flooding in the area, affecting 122,000 residents. The plan also offers an estimated 84 percent reduction in expected annual property damage while enhancing security at 262 critical infrastructure sites, 12 of which are considered essential to life safety. With the RP in place, the North Stockton impact area improves from an approximate 15 percent annual chance of flooding in the highest risk areas to less than 1 percent annual chance of flooding. The Central Stockton impact area improves from a 12 percent annual chance of flooding in the highest risk areas to an approximate 2 percent annual chance of flooding. Further information about specific Annual Chance of Exceedance probabilities and the performance of levees for a range of hydrologic events within su b-impact areas can be found in Appendix A: Economics .

The structural features of Alternative 7a include approximately 23 miles of levee improvements and two closure structures, one at Fourteen mile Slough and the other at Smith Canal. In addition t o the structural features, the RP also recommends the local sponsors complete a Floodplain Management Plan, including a Comprehensive Flood Warning Emergency Evacuation Plan to address residual flood risks.

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Figure ES-2: The Recommended Plan

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ENVIRONMENTAL EFFECTS
Environmental effects of the alternatives were evaluated in Chapter 5 of the document and are summarized in Table ES-5.

ESTIMATED COST AND COST SHARING
Investment cost accounts from the Micro Computer -Aided Cost Engineering System (MCACES) cost estimate for the RP are displayed in Table ES-2 below.

Table ES-2: Estimated Costs of Recommended Plan ($1,000) MCACES
Account2 Description Total First Cost1
01 Lands and Damages3

80,654

02 Relocations4 85,000
06 Fish and Wildlife 70,904
11 Levees and Floodwalls 566,599
15 Floodway Control and Diversion Structure 53,183
30 Planning, Engineering, Design6 144,901

31 Construction Management7 69,069
Total First Cost8 1,070,309
Notes:
1Based on October 2017 price levels, 2.75% interest rate, and a 50-year period of analysis. 2Micro Computer-Aided Cost Engineering System (MCACES) is the software program and associated format used by USACE in developing cost estimates. Costs are divided into various categories identified as “accounts.” Detailed costs estimates are presented in the Cost Engineering Addendum.
3Real Estate land costs, which include no damages.
4Relocations include relocating affected utilities
616 percent of 06, 11, and 15 accounts.
710 percent of 06, 11, and 15 accounts.
8 Numbers reported may be slightly different than those presented in the appendices due to rounding.

The refined benefits and costs of the RP are summarized in Table ES-3.

Table ES-3: Annual Costs and Benefits for Recommended Plan ($1,000) First Costs $1,070,309
Interest During Construction $231,829
Total Investment Cost $1,302,138
Interest and Amortization1 $48,232
OMRR&R $1,062
Total Annual Cost $49,294
Total Annual Benefits 345,024
Net Annual Benefits $295,730
Benefit to Cost Ratio 7.0
1October 2017 Price levels, 2.75% discount rate and a 50 year period of analysis.

ATTACHMENT D

Lower San Joaquin River
ES-15
Final Feasibility Report – January 2018
San Joaquin County, CA Executive Summary

Table ES-4 below shows the preliminary cost sharing for Alternative 7a. The NFS are reponsible for all Lands, Easements, Rights of Way, Relocations and Disposal Sites (LERRDs) costs, a minimum of 5 percent cash, and any additional cash needed to reach a minimum of 35 percent of the total project cost. The maximum non-Federal share is 50 percent of the total project cost.

Table ES-4: Summary of Cost Sharing Responsibilities for the Recommended Plan 1 ($1,000s - working level estimates)
MCACES
Account Item Federal1,2 Non-Federal1 Total1
01 Lands and Damages3 10,675 69,979

80,654

02 Relocations 0 85,000 85,000
06 Fish and Wildlife Facilities 70,904 0 70,904
11 Levees and Floodwalls 566,599 0 566,599
15 Flood Control and Diversion
Structure 53,183 0 53,183
30 Planning, Engineering, Design 144,901 0 144,901
31 Construction Management 69,069 0 69,069
Subtotal 907,575 154,979 1,070,309
Minimum 5% Cash Contribution 53,515
Additional Cash Contribution (219,629) 219,629
Subtotal (NED Plan Cost Sharing) 695,701 374,608
Cost Sharing (%) 65 35 100

Total (NED Plan Cost Sharing)4 695,701 374,608 1,070,309 Notes:
1 October 2017 price levels, 2.75% interest rate, and a 50-year period of analysis. 2 Federal Project First Costs are based on 65% of the NED Plan of $1,070,309,000. 3 Lands, Easements, Rights of Way, Relocations and Disposal Areas. 4Numbers reported may be slightly different than those presented in the appendices due to rounding.

MAJOR CONCLUSIONS
The recommendation of USACE is that the report be finalized based on results of public review, internal policy review, ATR and IEPR of this Final FR/ EIS/EIR, and if warranted, recommended for authorization and implementation funding as a Federal project. The estimated first cost of the recommended plan is $1,070,309,000 and the estimated annual operation, maintenance, repair, replacement, and rehabilitation (OMRR&R) costs are $1,062,000. The Federal portion of the estimated first cost is $695,701,000. The NFS portion of the estimated first cost is $374,608,000.

ATTACHMENT D

Lower San Joaquin River
ES-16
Final Feasibility Report – January 2018
San Joaquin County, CA Executive Summary

Table ES-5: Comparative Summary of Environmental Effects, Mitigation, and Levels of Significance Resource
Alternative 1
No Action Alternative 7a Alternative 7b Alternative 8a Alternative 8b Alternative 9a Alternative 9b Geology and Geomorphology
Effect No effect. No effect. No effect. No effect. No effect. No effect. No effect.

Significance Too speculative for
meaningful
consideration.

Less than significant. Less than significant. Less than significant. Less than significant. Less than significant. Less than significant.

Mitigation Not applicable. Not applicable. Not applicable. Not applicable. Not applicable. Not applicable. Not applicable.

Effect With
Mitigation
Not applicable. Not applicable. Not applicable. Not applicable. Not applicable. Not applicable. Not applicable.

Seismicity
Effect The structural integrity
of existing levees,
berms, and bridges
would remain at risk
from high magnitude
seismic events on active
faults. Some levees in
tidally influenced areas
would remain at risk
from seismically
induced structural
instability and/or failure
due to liquefaction.

Levee improvements
would reduce the
vulnerability to
structural failure due
to seismic events.

Significance Too speculative for
meaningful
consideration.

Less than significant. Less than significant. Less than significant. Less than significant. Less than significant. Less than significant.

Mitigation Incorporate seismic
design elements into
the FRM system.

Not applicable. Not applicable. Not applicable. Not applicable. Not applicable. Not applicable.

Effect With
Mitigation
Not applicable. Not applicable. Not applicable. Not applicable. Not applicable. Not applicable.

Not applicable.

ATTACHMENT D

Lower San Joaquin River
ES-17
Final Feasibility Report – January 2018
San Joaquin County, CA Executive Summary

Resource
Alternative 1
No Action Alternative 7a Alternative 7b Alternative 8a Alternative 8b Alternative 9a Alternative 9b Soils and Mineral Resources
Effect A flood event could
mobilize soils and
transport and deposit
them elsewhere in the
system. Mining
operations would
continue to be at risk
from flooding.

Short term soil
disturbance due to
construction
activities.

Significance Too speculative for
meaningful
consideration.

Less than significant. Less than significant. Less than significant. Less than significant. Less than significant. Less than significant.

Mitigation None possible.

Implement BMPs
during construction. At
the end of construction,
reseed disturbed areas
with native herbaceous
species.

Effect With
Mitigation
Not applicable. Less than significant. Less than significant. Less than significant. Less than significant. Less than significant. Less than significant.

Hydrology and Hydraulics
Effect Emergency repairs
during a flood event
could result in loss of
channel capacity and
alteration of current
geomorphic processes.

Closure structures
would reduce riverine
and tidal flow peaks to
produce beneficial
impacts by reducing
flood risk.

Significance Significant. Less than significant. Less than significant. Less than significant. Less than significant. Less than significant. Less than significant.

Mitigation None possible. None needed. None needed. None needed. None needed. None needed. None needed.

Effect With
Mitigation
Significant. Not applicable. Not applicable. Not applicable. Not applicable. Not applicable. Not applicable.

ATTACHMENT D

Lower San Joaquin River
ES-18
Final Feasibility Report – January 2018
San Joaquin County, CA Executive Summary

Resource
Alternative 1
No Action Alternative 7a Alternative 7b Alternative 8a Alternative 8b Alternative 9a Alternative 9b Water Quality
Effect In a flood event, there
is high risk of
contaminants entering
the water from utilities,
stored chemicals, septic
systems, and flooded
vehicles. Flood flows
would increase
turbidity in the
waterways through
bank erosion.

Potential impacts
include increased
turbidity during in-
water construction;
runoff of exposed soils;
and cement, slurry, or
fuel spills during
construction. Potential
long term water quality
impacts from closure
structures.

Potential impacts
include increased
turbidity during in-
water construction;
runoff of exposed soils
;
and cement, slurry, or
fuel spills during
construction. Potential
long term water quality
impacts from closure
structures.

Significance Too speculative for
meaningful
consideration.

Significant Significant Significant Significant Significant Significant and unavoidable.

Mitigation Construct levee
improvements and
related FRM
measures.

Preparation of a
Stormwater Pollution
Prevention Plan, Spill
Prevention Control and
Countermeasures Plan,
and a Bentonite Slurry
Spill Contingency Plan
and implementation of
BMPs. Develop design
and operation
refinements in
coordination with the
Regional Water Quality
Control Board
(RWQCB).

Preparation of a
Stormwater Pollution
Prevention Plan, Spill
Prevention Control and
Countermeasures Plan,
and a Bentonite Slurry
Spill Contingency Plan
and implementation of
BMPs. Develop
operation and design
refinements in
coordination with the
RWQCB.

Effect With
Mitigation
Not applicable. Less than significant Less than significant Less than significant Less than significant Less than significant Less than significant

ATTACHMENT D

Lower San Joaquin River
ES-19
Final Feasibility Report – January 2018
San Joaquin County, CA Executive Summary

Resource
Alternative 1
No Action Alternative 7a Alternative 7b Alternative 8a Alternative 8b Alternative 9a Alternative 9b Groundwater
Effect Continue to
implement
groundwater
management to
ensure adequate
recharge and
sustainable extraction
rates.

Potential construction-
related impacts if cutoff
walls penetrate into
groundwater.

Contaminants that
could reach
groundwater include
sediment, oil and
grease, and hazardous
materials.