Solvang City Council
January 10, 2022

0.0 ft elevati
ng curve ca
pth for any g
ntinuous RC
raphs, essen
s.
st Thalweg (RC
ght at 100 cfs f
26 runs,
riffle
ut not
uld be
ith its
Stage
ion at
an be
given
CT–Q
ntially
CT)
from
27 3.5 Adapting Riffle Crest Thalwegs to the Thompson Method for Estimating Minimum Adult Passage Streamflows
The next step for estimating a minimum passage streamflow was to identify a RCT depth that provided the TPM bookend minimum passage depth of 0.8 ft. For a familiar scale reference, two stacked 12 oz soda cans are almost exactly 9.6 inches (0.8 ft) high. With this RCT depth identified, we could use the RCT rating curves to estimate minimum passage streamflows and apply them to our adult steelhead passage opportunity analysis. The RCT depth providing 0.8 ft bookend minimum depths depended on the transverse slope at the riffle crest (Figure 9).

Mainstem LSYR riffles typically have 2% to 4% transverse slopes approaching from either bank’s active channel edge down to the thalweg (based on cross section profiles from the SYTAC 1999 passage field data and field observations). Using 0.8 ft (9.6 inches) as minimum passage bookend depths in our study, the 25% THP passage zone (which will require more streamflow than the 10% width TPM criterion) in an 80 ft wide uniform riffle with a 2% transverse slope (i.e., selecting an intermediate transverse riffle slope) would require a minimum RCT depth of 1.0 ft (Figure 9). Steeper transverse riffle slopes with the same transect length in a uniform riffle would result in greater minimum RCT depths. For example, a uniform 80 ft wide riffle with 5% right and left bank transverse slopes would require a minimum RCT depth of 1.3 ft deep to achieve the bookend 0.8 ft depths. Gentler slopes required shallower minimum RCT depths. For example, a uniform 80 ft wide riffle with 1% right and left bank transverse slopes would require a minimum RCT depth of 0.9 ft to achieve the 0.8 ft bookend depth. Therefore, we used an RCT depth of 1.0 ft to estimate the streamflow that provided bookend depths of

0.8 ft in the Thompson Method.

The final step was to estimate the minimum passage streamflow using the minimum RCT depth of 1.0 ft (thus achieving the 0.8 ft bookend depths of the TPM migration corridor). However, an adjustment to how we interpreted the constructed mainstem RCT-Q rating curves was necessary.

Mainstem alluvial riffle crests typically have very low baseflows seeping through them, rather than over them as surface flow. At an upstream gage plate located in a pool or run, the change in water surface elevation (i.e., in stage height on the gage plate) between 0 cfs and 1 cfs can be 0.2 ft or more. In the ‘H’ Street nr Lompoc Q-Stage rating curve the stage difference was 0.20 ft. 28 Using our methodology for converting USGS Stage-Q rating curves into RCT-Q rating curves at the downstream riffle crest (Figure 10), 1 cfs would be assigned an RCT depth of 0.20 ft for the ‘H’ Street RCT-Q rating curve. But at very low baseflows, such as 1 cfs flowing through a mainstem riffle with an upstream drainage area of almost 800 mi2 at the ‘H’ Street gage location,
seepage will transform the 0.18 ft flow depth (predicted by the RCT-Q rating curve) into a much shallower streamflow best characterized as ‘oozing through’ the riffle. To account for seepage, we kept the arbitrary elevation of gage plate stage for 0 cfs equal to 0 ft on the converted RCT-Q rating curves, but we relied on the gage plate stage at 1 cfs (then converted to depth on the RCTQ rating curve) as our functional 0 ft depth baseline from which to estimate the RCT depth for adult steelhead passage.

Given Bradbury Dam eliminates anadromous spawning habitat and adult access farther upstream, two mainstem USGS locations downstream of Bradbury Dam, at Solvang and nr Lompoc (Figure 1), were selected for measuring and assessing Adult Passage Opportunity Days.

Both locations required a USGS Q-Stage rating curve to construct a RCT-Q rating curve and estimate an adult passage streamflow with a 1 ft deep RCT.

A Contemporary USGS Q-Stage rating curve at Solvang (WY2012) was used to construct an RCT-Q rating curve. A gage height of 4.19 ft for 0 cfs and 4.37 ft for 1.0 cfs. These were adjusted to an RCT depth of 0 ft at 0 cfs and 0.18 ft at 1.0 cfs (Figure 11). Adding 1.0 ft of depth to RCT = 0.18 ft gave an RCT depth of the Solvang RCT-Q rating curve of 1.18 ft deep equivalent to a streamflow of 63 cfs.

Figure 11.

Q-Stage ra
Two Con
used to c
Stage rat

0.98 cfs.
(Figure 1
Narrows
ft for ~1.

1.0 cfs (F
RCT-Q rating
ating curve.
ntemporary U
construct RC
ting curve (I
These gage
12). Adding
nr Lompoc’
.0 cfs (Figur
Figure 13). A
curve construc
USGS Q-St
CT-Q rating
D No. 0005
heights wer

1.0 ft of de
’ USGS Q-S
re 13). Thes
Adding 1.0 ft
cted from USG
age rating c
g curves for
, WY2012)
re adjusted to
epth to RCT
Stage rating c
e were adju
ft of depth to
GS Gaging Stat
urves near L
the Lompo
had a gage h
o an RCT de
T = 0.20 ft
curve had a g
sted to an R
o RCT = 0.18
tion No. 11128
Lompoc (Fig
oc Floodplai
height of 1.5
epth of 0 ft a
gave a strea
gage height
RCT depth o
85 ft gave a
8500 Santa Yne
gure 12 and
in. The ‘H’
50 ft for 0 c
at 0 cfs and 0
amflow of 1
of 1.96 ft fo
f 0 ft at 0 cf
streamflow
ez River at Solv
d Figure 13)
Street USG
cfs and 1.70

0.20 ft at 0.9
101 cfs. Th
or 0 cfs and 2
fs and 0.185
of 88 cfs.
29 vang
were
GS Qft for
98 cfs
he ‘at

2.145
5 ft at

Figure 12.

Ynez River
Figure 13.
nr Lompoc
RCT-Q rating
at ‘H’ Street n
RCT-Q rating
c Q-Stage ratin
curve construc
nr Lompoc Q-S
curve construc
g curve for WY
cted from USG
Stage rating cu
cted from USG
Y 2012.

GS Gaging Stat
urve for WY20
GS Gaging Stat
tion No. 11134

12. tion No. 11133
4000 Santa Yne
00 Santa Ynez
ez River at San
z River at Narr
30 nta
ows
31 3.6 Minimum Adult Passage Streamflows Using RCT‐Q Rating Curves In our adult steelhead passage analysis, an adult passage opportunity day at Solvang occurred when Q equaled 63 cfs or greater. Near Lompoc, an adult passage opportunity day occurred when Q equaled 101 cfs or greater at the ‘H’ Street Lompoc location and when Q equaled 88 cfs or greater at the Narrows near Lompoc. The higher streamflow of 101 cfs, and therefore more limiting passage streamflow, was selected for the passage opportunity analysis representing the Lompoc Floodplain.

Higher minimum passage streamflows in the Lompoc Floodplain, than at Solvang, were expected because of differences in channel morphology. However, we thought the differences would have been greater than estimated. Above the Narrows, the mainstem LSYR has a more pronounced alternate bar morphology with more prominent low streamflow hydraulic controls.

Extensive woody riparian encroachment into the active channel, fed by more reliable surface flows through summer, also influences this Q-Stage relationship. It can rapidly change with one big scouring flood. In contrast, the finer grained mainstem below Robinson Bridge in the Lompoc Floodplain has a relatively weak expression of an alternating bar morphology. Confined flood flows help keep woody riparian encroachment from becoming too dominant a force controlling baseflow stage heights.

With only a few USGS Q-Stage rating curves available, variability in RCT depth among many riffles at the same streamflow (e.g., at the 101 cfs minimum passage streamflow at ‘H’ Street) and in transverse riffle slopes (ranging from 0.5% to 5%) could be evaluated on the SYR when there is ample streamflow (not the situation during our study). A systematic survey of RCT depths in the Lompoc Floodplain from approximately 200 cfs to 1 cfs (taking a minimum of 8 depth measurements) at 10 to 15 riffle crests could be accomplished within a single runoff event.

A plus/minus change of 0.1 ft RCT depth at ‘H’ Street, as computed to estimate the adult passage streamflow, would result in a range of 80 cfs to 125 cfs (Figure 12). This streamflow range should be expected for a minimum passage streamflow because separate RCT-Q rating curves for 10 riffles or more, all within one geomorphically similar mainstem reach, will still exhibit considerable natural variability.
32 A recommended passage streamflow should anticipate complicating factors and natural geomorphic variability (e.g., no mainstem channel at a given streamflow will have all its riffles flowing at the same depth). Channel hydraulics change as woody riparian vegetation encroaches into the actively scoured channel (the channel width targeted in the Thompson Method) during successive years experiencing only low-scouring storm peaks. The 2008 Annual Monitoring Report and Trend Analysis for 2005-2008 (US Bureau Reclamation 2011) provides photographs of the same mainstem location and perspective in Lower SYR in May 2005 and again in October 2007 (US Bureau Reclamation 2011, Figure 26 on p. 70). Woody riparian encroachment captured by Photo Point M-19 at Avenue of the Flags Bridge will have increased water stage, especially by encroaching across riffle crests (creating a minor backwater effect upstream at very low streamflows) and along point bar margins in only 2 plus years. RCT-Q rating curves through the Lower SYR, will be changing constantly depending on recent and future flooding. Recentlyscoured bar features will require higher streamflows before achieving a desired riffle depth for estimating an adult steelhead passage opportunity day.

3.7 Annual Adult Steelhead Passage Opportunity Days in the Lower Santa Ynez River
The most straightforward measure for quantifying adult steelhead migration potential in the mainstem SYR was the total number of passage opportunity days tallied each migration season within each regulatory period. Two mainstem locations were selected: close to Bradbury Dam at Solvang and distant from Bradbury Dam near Lompoc. Minimum adult steelhead passage streamflows of 63 cfs at Solvang and 101 cfs at ‘H’ Street near Lompoc defined an Adult Steelhead Passage Opportunity Day. Each WY’s adult steelhead migration season was triggered by the first daily average streamflow at the Lompoc USGS gaging station exceeding approximately 800 cfs (following December 15) for opening the SYR Lagoon and ended each year on April 30. Fry would not be emerging form redds constructed after April 30 Migration no sooner than mid-June and would not likely contribute to population recovery.

Annual spawning opportunity days (Y-axis) were plotted by Total Annual Precipitation Exceedence (P-value on X-axis) (Table 1) for each water year within the Pre-Gibraltar Dam, Gibraltar Dam, and Cachuma Dam/Bradbury Dam regulatory periods at ‘H’ Street (Lompoc Floodpla
Figure 19
line estab
value wa
all adult p
Figure 14.

Gibraltar
ain) (Figure
9). A lower
blished that
as usually gr
passage opp
. Annual Adul
Dam Period b
14, Figure
bound was
total annua
eater. Given
portunity plot
lt Steelhead P
by water year
15, and Fig
fit to each p
al number of
n judgment w
ts were inclu
assage Oppor
with lower bo
gure 16) and
plot limited
f passage op
was exercise
uded.
rtunity Days in
ound line.
d at Solvang
to two line
pportunity d
ed in delinea
n the Lompoc
g (Figure 17
segments. T
days for any
ating these lo
c Floodplain d
7, Figure 18
The lower b
y given WY
ower bound
uring the Pre33
8, and
bound
Y’s Plines,
-
Figure 15.

Period by
Figure 16
Cachuma/
. Adult Steelhe
water year w
. Adult Steelh
/Bradbury Da
ead passage O
ith lower boun
head Passage
am Period with
Opportunity D
nd line.

Opportunity
h lower bound
Days in the Lom
Days in the L
d line.
mpoc Floodpl
Lompoc Flood
ain during th
plain by wat
e Gibraltar D
er year durin
34 am
ng the
Figure 17
hydrograp
Figure 18
Period wit

7. Adult Stee
phs from WY1
. Adult Steelh
th lower boun
elhead Passag
1942 to WY20
head Passage
nd line.
ge Opportun
012 with lower
Opportunity
nity Days at
r bound line.

Days at Solva
Solvang for
ng by water
r estimated u
year during
nimpaired a
the Gibraltar
35 nnual
r Dam
Figure 1
Cachuma/
P-values
days to a
Street (F
WYs we
15 (Gibra
P-values
expected
Figure 15
winter,
measurem
baseline
daily ave
daily mig
(the reco
Days we
baseline

9. Adult St
/Bradbury Da
exceeding 7
attempt a lo
Figure 14) m
re available
altar Dam P
exceeding 4
d because of
5 relative to
small flood
ments durin
(total annua
erage stream
gration seaso
ord history a
ere tallied fr
at Solvang (
teelhead Pas
am Period with
70% (i.e., Dr
ower bound
might not ad
, the line mi
eriod at ‘H’
40%. A simi
f the low st
Figure 14 a
d hydrogra
ng the Pre-G
l passage da
mflows on Sa
on streamflo
t the USGS
from these e
(Figure 17).
sage Opport
h lower bound
ry and Critic
fit. The sho
dequately de
ight be place
Street) prod
ilar lower bo
torage capac
also was exp
aphs. Solva
Gibraltar Da
ays with no d
anta Cruz C
ows were est
Santa Cruz
estimated un
tunity Days
d line.
cally Dry W
ort WY reco
fine a lower
ed lower). H
duced a simi
ound in wet
city of Gibr
pected becau
ng only h
am Period,
dam regulati
Creek (metho
timated for S
gaging stati
nimpaired h
at Solvang
WYs in Figur
ord for Pre-G
r bound line
However, the
ilar line in w
t years (betw
raltar Reserv
use Gibraltar
had a few
and therefo
on) to comp
od described
Solvang betw
ion). Annua
hydrographs
by water
re 4) had too
Gibraltar Da
e (i.e., if mo
e lower bou
wet years bu
ween Figures
voir. A low
r Dam could
miscellane
ore prevente
pare lower bo
d in Section
ween WY19
al Adult Pass
to establish
year during
o few opport
am Period a
ore Pre-Gib
und line in F
ut a lower lin
s 14 and 15)
wer bound lin
d influence e
eous stream
ed establishi
ound lines. U

2.3), unimp
942 and WY
sage Opport
h a lower b
36 g the
tunity
at ‘H’
braltar
Figure
ne for
) was
ne in
earlymflow
ing a
Using
paired
Y2012
tunity
bound
37 Gibraltar Reservoir has a much lower storage capacity than Cachuma Reservoir and regulates considerably less of the SYR Basin. Gibraltar Dam controls 50.9 % (= 219 mi2 /430 mi2 * 100) of
the headwaters (upstream of San Lucas Bridge) compared to Bradbury Dam controlling 97.7 % (= 420 mi2/430 mi2 * 100). Annual Adult Passage Opportunities were therefore considerably more impacted by the additional of Bradbury Dam in the 1950s. But Extremely Wet WYs were not significantly affected. The Solvang lower bound at P = 10% was 82 during the Pre-Gibraltar Dam passage opportunity days during the Pre-Gibraltar Dam Period (Figure 17), 82 days during the Gibraltar Dam Period (Figure 18), and 65 days during the Cachuma-Bradbury Dam Period (Figure 19).

The most notable trend, however, was not with respect to the lower bound lines but with the variability in annual total passage opportunity days for P-values greater then approximately 40% at Solvang and ‘H’ Street. At Solvang in Blw-Average WYs (P-values between 50% and 70%), the variability in total passage days declines sharply with increasing flood management and reservoir storage capacity. Under Pre-Gibraltar Dam conditions, total annual passage days ranged from 0 days to approximately 80 days at P = 60% (Figure 17), 0 days to approximately 60 days in the Gibraltar Dam Period (Figure 18), down to 0 days to approximately 8 days in the Cachuma-Bradbury Dam Period (Figure 19). Adult steelhead in Blw-Normal WYs once encountered ample opportunities to deliver their eggs. A few days of QMinPass might not have been sufficient to allow spawning adults to reach the upper headwaters (assuming no dams), but a few passage days would make a difference accessing Hilton Creek.

The three lower bound lines, corresponding to the three regulatory periods, were plotted together for Solvang and Lompoc (Figures 20 and 21). Lompoc at the ‘H’ Street USGS gage was expected to have fewer passage days than Solvang because the QMinPass streamflow at Lompoc was 101 cfs whereas at Solvang it was 65 cfs. But the analysis suggested otherwise. For example, the annual number of passage opportunity days on the lower bound line for P = 30% at Solvang during the Cachuma-Bradbury was 17 days (Figure 21) and 16 days (Figure 20) at ‘H’ Street.

Figure 20
during the
Figure 21.

Dam and
hydrograp

0. Lower boun
e Pre-Gibralta
. Lower bound
Cachuma/Br
phs.
nd lines for A
ar Dam, Gibra
d lines for Ad
radbury Dam
Adult Steelhe
altar Dam, an
ult Steelhead
m periods, and
ead Passage O
nd Cachuma/B
Passage Oppo
d for estimat
Opportunity D
Bradbury Dam
ortunity Days
ted unimpaire
Days in the L
m periods.
s at Solvang d
ed WY1942 t
Lompoc Flood
uring the Gib
to WY2011 a
38 dplain
braltar
annual
39 3.8 Conclusions
Figures 22 and 23 summarize the percent losses in Total Annual Adult Passage Days at Solvang and ‘H’ Street relative to their respective Pre-Gibraltar baselines. Based entirely on the total number of annual passage opportunity days applied to Solvang (QMinPass = 63 cfs) and ‘H’ Street (QMinPass = 101 cfs), the Gibraltar Dam Period had a relatively minor impact on adult steelhead migration (an overall 5% loss) compared to an overall 50% loss during the Cachuma-Bradbury Dam Period in wet years at ‘H’ Street (Figure 23). In large part, this outcome was attributable to Lake Cachuma Reservoir’s larger capacity, and therefore greater efficiency, at capturing flood events. In Above-Normal and Below-Normal WYs both regulatory periods were affecting adult passage. The Gibraltar Dam Period reduced annual passage opportunity days at ‘H’ Street by approximately 44% in Below-Normal WYs and by approximately 88% during the CachumaBradbury Dam Period (Figure 23). Loss in variability of Total Annual Adult Passage Days, particularly at P-values less than 50% but in wetter WYs as well (Figures 14 through 19), may be more a factor restricting future recovery than trends in the lower bound lines.

Figure 22
regulatory
Figure 23
regulatory

2. Adult steel
y period.

3. Adult steel
y period.
head passage
head passage
e opportunity
e opportunity
losses of the
losses of the
e lower boun
lower boun
d line at So
d line at Lo
lvang during
ompoc during
40 g each
g each
41 3.9 Bradbury Dam Effects on Passing Floods
Dam spills occur when Lake Cachuma Reservoir is full, with the operational objective of minimizing spills to the greatest extent possible. The 2010 Monitoring Report (U.S. Bureau of Reclamation 2013), summarizing dam spills during the Contemporary Bradbury Dam Period, documents spills during WY2001, WY2005, WY2006, and WY2011. These spills (Figure 24) provided a large share of the total passage opportunity days in their respective WYs. WY2006 had a low total of passage opportunity days because the spill was late in the migration season.

The monitoring report (U.S. Bureau of Reclamation 2013) does not quantify floods originating above Bradbury Dam and Gibraltar Dam that are captured entirely by Lake Cachuma Reservoir and therefore these floods cannot contribute to adult passage downstream of Bradbury Dam.

USGS Gaging Station No. 11124500 Santa Cruz Creek nr Santa Ynez located upstream of Bradbury Dam but downstream of Gibraltar Dam (Figure 1) has been monitoring unimpaired daily average streamflows since WY1942 (as discussed in Section 2.3). USGS’s monitoring also included flood flows. In each annual report, the date, time, stage, and instantaneous peak magnitude of all floods are summarized. A minimum base flood of 100 cfs was established for the USGS Santa Cruz Creek Gaging Station, meaning only flood peaks with instantaneous peak discharges greater than 100 cfs are considered floods. These flood events are often referenced as ‘partial floods’ as opposed to gaging stations reporting the more traditional largest flood peak for the water year. The recording of partial floods, therefore, provided the opportunity to determine which floods passed through Bradbury Dam and which were captured.

All partial floods beginning WY2000 (start of the Contemporary Bradbury Dam Period) were inventoried. To determine whether a particular flood had spilled, USGS Gaging Station No. 11125500 Lake Cachuma nr Santa Ynez provided daily Lake Cachuma Reservoir ac-ft volumes (related to reservoir stage) to determine whether the reservoir was ‘full’ on the day each flood event arrived at the reservoir. A total of n = 52 floods were recorded at the USGS Gaging Station No11124500 Santa Cruz Creek nr Santa Ynez from WY2000 through WY2012 (Figure 24).

Bradbury Dam spilled 13 times (25%), including the 4 largest peak events.

Figure 24.

Santa Yne
Bradbury
Unit runo
drainage
peak inst
relative t
an instan
would be
Dam equ
event, the
peak.
. Flood peaks
ez (DA = 74 m
Dam Period.
off of Santa
area above
tantaneous f
to the same
ntaneous pea
e approxima
ually contrib
e weighted p

(instantaneou
mi
2 ) that were
Cruz Creek
Bradbury D
flow. This w
event gener
ak flow of a
ately equival
buted (i.e., (
peak was 57
us peak cfs) a
e spilled, and
k’s peak inst
Dam (DA =
was done to
ated by tribu
1000 cfs Sa
lent to a 570
1000 cfs / 7
70 cfs; for a
at USGS Gagi
not spilled, b
antaneous fl
420 mi2) to
better contr
utaries down
anta Cruz Cr
00 cfs event
74 mi2) * 42
200 cfs Sant
ing Station No
by Bradbury
lows (i.e., cf
o approxima
rast the imp
nstream of B
reek peak ev
t if the entir
20 mi2 = 56
ta Cruz Cree
o. 11124500 S
Dam during
fs/mi2) was m
ately quantify
portance of
Bradbury Da
vent (the flo
re watershed
676 cfs). Fo
ek peak, a 1
Santa Cruz Cre
the Contemp
multiplied b
fy the unimp
each flood
am. In Figur
ow on the yd above Brad
or a 100 cfs
140 cfs weig
42 eek nr
porary
by the
paired
event
re 24,
-axis)
dbury
peak
ghted
43 WY2010 was noteworthy given its Wet WY type (P = 23.7%) but poor total passage opportunity performance (n = 37) (Figure 19). This total plotted close to the lower bound line (Figure 19).

Although no single flood peak was big (Figure 19) they were numerous but also entirely captured by Cachuma Reservoir. Collectively these flood peaks would have, without Bradbury Dam, produced many passage opportunity days at Solvang and Lompoc. For a WY with the same P = 24% at Solvang during the Gibraltar Dam Period, the lower bound line for total passage days was 54 (Figure 18). But perhaps more importantly, these flood peaks prior to Bradbury Dam would have gotten adult steelhead into the LSYR early in the migration season and allowed them to stage near tributary confluences for the next high flow event.

In WYs with spills from Bradbury Dam, there were often one or more smaller flood events, not spilled, that preceded a considerably bigger event that spilled (e.g., WY2001, WY2006, WY2008, and WY2011). Without Bradbury Dam, these smaller floods earlier in the migration period could have caused the SYR Lagoon to open earlier (and keep it open longer) and helped stage adults for the big event soon to come (thus maximizing the opportunity to reach the upper reaches of the tributary watersheds). This would have helped avoid migration delay inevitably associated with the first spawning event of the season; adults must swim up to a tributary but start at the SYR Lagoon, arriving several days after tributaries have peaked (addressed in next section).

Fewer floods downstream of Bradbury Dam have meant fewer minimum passage opportunity days. As an example of how many fewer days, two rainfall/runoff hydrographs from WY2003 at Solvang were compared with the following three flow scenarios: (1) Gaged streamflows at USGS Gaging Station No.11128500 Santa Ynez River at Solvang (i.e., with Bradbury Dam), (2) Estimated streamflows with Gibraltar Dam (i.e., without Bradbury Dam), and (3) Estimated PreGibraltar streamflows (i.e., without Gibraltar and Bradbury dams). Neither event spilled.

Hydrographs were constructed for each rainfall/runoff event using the unit runoff approach discussed previously.

The first rainfall/runoff event for WY2003 occurred December 18 to 26, 2002 (w/ QPeak at Santa Cruz Creek = 253 cfs, and weighted unimpaired QPeak = 1440 cfs) (Figure 25). The following number of minimum passage opportunity days (QMinPass = 63 cfs at Solvang) for each flow scenario
Gibraltar
season ev
Figure 25
that occur
Gibraltar
The seco
Santa Cr
following
flow scen
w/Gibral
Bradbury
was: minim
r Dam = 5 d
ven the unim
. Rainfall/run
rred Decembe
Dam, and (3)
ond rainfall/r
ruz Creek =
g number of
nario was: m
ltar Dam = 7
y dams) = 24
mum passage
days, and mi
mpaired hydr
noff hydrograp
er 18 to 26, 20
without Gibr
runoff event
= 868 cfs a
f minimum p
minimum pa
7 days, and m
4 days.
days with B
inimum pass
rograph rece
phs at USGS
002 modeled
raltar and Bra
t in WY2002
and weighte
passage opp
assage days
minimum pa
Bradbury Dam
sage days P
ded quickly
Gaging Statio
for three flow
adbury dams.
2 occurred M
d unimpaire
ortunity day
w/Bradbury
assage days
am = 4 days,
Pre-Gibraltar
.
on No.111285
w scenarios: (1
March 14 to
ed QPeak =
ys (QMinPass =
y Dam = 2 d
Pre-Gibralta
minimum p
r Dam = 7 d
500 Santa Yne
1) with Bradb
o April 19, 2
4930 cfs) (
= 63 cfs at S
days, minimu
ar Dam (wit
passage days
days. Early i
ez River at So
bury Dam, (2
2002 (w/ QP
(Figure 26).

Solvang) for
mum passage
thout Gibralt
44 s with
in the

olvang
) with
Peak at
. The
r each
days
tar or
Figure 26
three flow
Bradbury
Hydrogra
(Figure 2
and grou
watershe
runoff at
drainage
– 219 mi
area. Pea
migration
. Rainfall/run
w scenarios: (
dams.
aphs for the
25 and Figu
undwater d
d) given the
the USGS S
area above
i
2 to simulat
ak runoff la
n benefit per
noff hydrogra
(1) with Brad
two rainfall
re 26). The
downstream
ere were no
Santa Cruz g
Bradbury D
te Gibraltar
ater in the s
r ac-ft later i
phs at Solvan
dbury Dam,
l/runoff even
gaged hydr
of Bradbu
spills in W
gaging statio
am (420 mi2
Dam captur
eason will p
n the migrat
ng that occur
(2) with Gib
nts show the
rograph at S
ury Dam (a
WY2003. The
n, the unimp
2 ) and the G
ring all the
produce mo
tion season).
red March 14
braltar Dam,
e consequenc
olvang was
an approxim
e other two
paired hydro
Gibraltar hydr
flood flow o
ore passage
.
4 to April 19
and (3) with
ces of differ
derived fro
mate 150 m
were model
ograph weigh
rograph wei
originating f
opportunity
, 2002 modele
hout Gibralta
rent flow reg
om surface ru
mi
2 contrib
led from the
hted by the e
ghted by 42
from its dra
days (i.e.,
45 ed for
r and
gimes
unoff
buting
e unit
entire
0 mi2
inage
more
46 4 Spawning Opportunity and Upstream Migration Model

4.1 Introduction
Each spawning habitat location below San Lucas Bridge became much more important when Bradbury Dam eliminated all anadromous spawning habitat above San Lucas Bridge. A steelhead spawning migration model was developed to assess steelhead spawning potential and success in the Lower Santa Ynez River under Cachuma/Bradbury Dam Period annual hydrographs. Salsipuedes Creek (a tributary to the Lower Santa Ynez River) was selected for this analysis because it is a large unregulated tributary readily accessible to spawning adult steelhead with relatively good juvenile rearing habitat and persistent summer streamflows.

Assessing spawning success at a specific destination required completing two sequential tasks.

First, every day during the migration season of each water year was assessed for its potential to provide ample spawning habitat should an adult arrive and, if a redd was built, that it would successfully incubate the eggs until fry emergence (using a 40-day incubation period based on Barnhart 1986). A day that could accomplish both was labeled a Low Risk Spawning (LRS) day.

Next, a migration model was constructed to route spawning adults from the Santa Ynez Lagoon to spawn in a desired destination. Each LRS day that an adult steelhead could have actually arrived at the spawning destination was counted as a Successful Spawning Opportunity (SSO) day by the model. Within the Salsipuedes Creek Watershed, three steelhead spawner destinations were selected for assessing spawning potential and spawning success: (1) Lower Salsipuedes Creek at the USGS gage Station No. 11132500 Salsipuedes Creek nr Lompoc (RM

20.1), (2) El Jaro Creek 1.8 miles above the Los Amoles Creek confluence (RM 25.6), and (3) Los Amoles Creek one mile upstream from its confluence with El Jaro Creek (RM 24.8) (Figure 27).

Figure 27.

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48 threshold (Table 2) to ensure ample and diverse spawning habitat locations. The 15 cfs streamflow threshold on Lower Salsipuedes Creek (Table 2) had an RCT depth of 0.50 ft. No upper streamflow threshold for spawning habitat availability was modeled. The redd incubation streamflow threshold (i.e., a streamflow below this value occurring during the incubation period would kill the eggs) also was conservatively high to target higher quality redd locations. The 3 cfs redd incubation streamflow threshold for Lower Salsipuedes Creek (Table 2) had a RCT depth of approximately 0.25 ft. The 40-day redd incubation period was conservatively short (50- day to 60-day or longer in colder streams to the north) (Barnhart 1986), but attempted to account for the likelihood that southern California steelhead would be more tolerant of higher water temperatures that would slightly accelerate egg incubation times. Overall, total annual LRS days quantified the spawning potential of the destination for a specific water year independent of steelhead migration (which was considered in estimating total annual SSO days). A more sophisticated model, backed by field investigation, would include: (1) a redd scour threshold based on the partial instantaneous flood peaks included in USGS gaging records for Lower Salsipuedes Creek, (2) hourly streamflows rather than daily average, and (3) continuous water temperatures for adjusting redd incubation time and model whether emerging fry would encounter a hostile thermal environment on emergence.

Table 2. Low Risk Spawning (LRS) day parameters. Each spawning destination used a maximum incubation period of 40 days.

Spawning
Destination
Total Miles
from Ocean
Watershed Area
at Spawning
Destination (mi2
)
Spawning Habitat
Availability
Threshold (cfs)
Minimum Redd
Incubation
Threshold (cfs)
Lower
Salsipuedes Creek 20.1 47.1 15.0 3.0
El Jaro Creek 25.6 21.1 10.0 2.0
Los Amoles Creek 24.8 4.3 5.0 0.5
Alisal Creek 46.7 11.6 5.0 0.5

4.3 Estimating Steelhead Successful Spawning Opportunity Days A spawning adult steelhead must be able to arrive at a spawning destination on a LRS day for that day to be recorded a SSO day. A migration model was needed to predict whether an adult steelhead leaving the Santa Ynez Lagoon on a given day could arrive at a specified spawning 49 destination on a LRS day. The total number of SSO days was considered a measure of how well the watershed (from the Lagoon upstream to the spawning destination) performed in any given water year. High performance meant that migrating steelhead adults were capable of arriving to a spawning destination on most LRS days. Migration delays, natural or man-made, downstream of the spawning destination could result in fewer annual SSO days. Thus, this analytical approach was capable of assessing the effect of migration delay on steelhead spawning success. The model examined adult steelhead leaving the Santa Ynez Lagoon and migrating to three designated spawning destinations within Salsipuedes Creek Watershed from WY1942 to WY2012.

4.4 A Tool for Measuring Steelhead Spawning Success: An Adult Steelhead Migration Model
The Adult Steelhead Migration and Spawning Model was developed for this study, but could be adapted to other rivers. The model (Figure 28) worked by first reading an input file containing all model parameters and information needed for each model run. The model was coded in the Fortran90 language and compiled using the GFortran compiler (GNU Fortran project). A series of subroutines read-in the streamflow data from available gages, augmented the streamflow for intermediate reaches based on the unit runoff from gaged streamflows, converted streamflow into RCT (riffle crest thalweg) depths based on a reach-specific RCT-Q rating curve, and assigned an hourly migration rate to each reach each day. Then for each specified model run, LRS days were determined from the model parameters for spawning habitat availability and a minimum redd incubation streamflow threshold. A migration rate was assigned each day in each reach along the migration route to a specific spawning destination. Migration success was determined by routing the modeled steelhead from the starting location, through the reaches and segments to the spawning destination. SSO days were then determined by counting the modeled LRS days that could have been reached by a migrating adult within a 30-day migration period.

Lastly, the model generated user defined output files which were used to assess the model runs.

4.4.1 Streamflow Estimation along the Adult Steelhead Migration Route River mile increments for each reach along the migration route were calculated in ArcMap software (version 10.1, ESRI, Redlands, CA). Daily average streamflows for Lower Salsipuedes Creek (Figure 27) were provided by USGS Gaging Station No. 11132500 Salsipuedes Creek nr 50 Lompoc dating back to April 1, 1941. Steamflow for tributary reaches above the Lower Salsipuedes Creek USGS gage (in El Jaro and Los Amoles creeks) were estimated by unit runoff multiplied by the drainage area of the spawning destination. Daily streamflow in the SYR mainstem below Salsipuedes Creek was more complex. USGS gaging records were used to compile a streamflow record between the mouth of Salsipuedes Creek and Santa Ynez Lagoon from WY1942 to the present.

Figure 28. Flow chart of Adult Steelhead Migration and Spawning Model with major subroutines and their purposes. 51 52

4.4.2 Estimation of Daily Average Migration Rates from Riffle Crest Thalweg (RCT) Depths along the Migration Route
The RCT-Q rating curve for each mainstem and tributary segment from Santa Ynez Lagoon up to the spawning destination was applied to Figure 29 for assigning daily average migration rates for routing adult steelhead to their spawning destination. The scientific literature provides little guidance for estimating daily average steelhead migration rates in streams similar to Salsipuedes Creek or the mainstem Santa Ynez River. Instead, professional judgment was used to construct Figure 29. In February and March 2013, we observed adult steelhead migrating up cobble and small boulder streams in Humboldt County at streamflows with RCT depths between 0.40 ft and

0.25 ft at similar migration rates in Figure 29. Although these data do not provide migration rates, upstream fish trapping on Salsipuedes Creek (US Bureau Reclamation 2011, Table 12, p. 75) recorded adult steelhead upstream migration at 5.6 cfs, 5.2 cfs, and 3.4 cfs. These low baseflows were equivalent to RCT depths of 0.32 ft to 0.27 ft. Given the necessity of applying professional judgment, a sensitivity analysis (reported later in this Chapter) evaluated a range in daily average migration rates to quantify the effect on predicted total annual SSO days.

Dr. Craig Fusaro (pers. comm. 2012) mentioned meeting an older resident named Lyle Wolford who once lived at Cachuma Village, immediately below Bradbury Dam. Woldford related that once the sandbar broke open at Surf, it was 10 to 11 days before he saw spawners in Hilton Creek, between his cabin and the dam. The way Wolford phrased it, this wasn't an observation of a particular year, but an estimate of "average" travel time over decades of observation on variations. This observation gives a daily average migration rate of approximately 5 mi/day. The migration rates are meant to describe a sustained migration rate and do not represent maximum speeds but maximum number of miles that could be traveled over an entire day. 53 Figure 29. Relationship of daily average migration rate (miles/day) to the RCT depth (ft) used for migration routing from the Santa Ynez Lagoon to the spawning destinations in Salsipuedes Creek watershed.

4.4.3 Setting Maximum Allowable Travel Days
The maximum allowable travel days to complete migration from the Santa Ynez Lagoon upstream to the spawning destination was set at 30 days. If the model’s routing of a steelhead exceeded 30 days, that starting date at the Santa Ynez Lagoon could not qualify as an SSO day.

4.4.4 Modeling Steelhead Migration into Salsipuedes Creek Watershed The farther a potential migrating steelhead was from the confluence of a tributary to the mainstem SYR, the greater the risk that favorable migration conditions (primarily sufficiently deep RCT depths) might not prevail for an adult to reach the targeted spawning destination within the allotted 30 days. Not only must an adult steelhead travel farther and longer to reach a spawning destination tucked into a headwater tributary, but streamflows will sharply decline (and rapidly become shallow) due to shrinking watershed area along the migration route. In the model, migration success and number of migration days were determined by converting the daily average streamflow to RCT depth and applying the RCT depth/migration rate relationship to determined accumulated miles towards the spawning destination. The migration rate changed 0 0.2 0.4 0.6 0.8 1 1.2
0 1
2 3
4 5
6 Riffle Crest Depth at Thalweg (ft)
Migration Rate (miles/day)
Mainstem Santa Ynez
Tributaries
54 based on the daily streamflow and the location within the watershed. Migration routing used an hourly time step to evaluate the current day and position within the watershed. However, the available USGS data are reported as daily average streamflows and do not reflect streamflow fluctuations over the day.

4.5 Assessing Low Risk Spawning Days and Successful Spawning Opportunity Days in Salsipuedes Creek Watershed
Total Annual LRS days and Total Annual SSO days were quantified for WY1942 through WY2012 at the three spawning destinations in the Salsipuedes Creek watershed. Total LRS and SSO days were plotted with the water years arranged chronologically on the X-axis (Figure 30, Figure 31 and Figure 32) and as a function of Total Annual Precipitation Exceedence (P, %) (Figure 33, Figure 34 and Figure 35). On all six figures, a blue square represented a SSO day and a red triangle represented a LRS day that never became a SSO day.

F
S
igure 30. Low
R
Salsipuedes Cree
k
isk Spawning (
k (WY1942 to W
Y
LRS) da
ys (red
2012) b
y water ye
triangles) and
S
ear.
pawning Success Opportunit
y (SSO) da
ys (blue squares) modele
d
55 for Lower
F
(
igure 31. Low
R
(WY1942 to WY2
isk Spawning (L
R
012) b
y water
yea
RS) da
ys (red tria
ar.
ngles) and Spa
wning Success Op
portunit
y (SSO)
days (blue squares) modeled for El
56 Jaro Creek
F
(
igure 32. Low Ri
(WY1942 to WY2
sk Spawning (L
R
012) b
y water
yea
RS) da
ys (red tria
n
ar.
ngles) and Spawning Success Opportunit
y (SSO) da
ys (blue squares)
modeled for Los
A
57 moles Creek
F
S
igure 33. Low
R
Salsipuedes Cree
k
isk Spawning (
k vs precipitation e
LRS) da
ys (red
xceedence (WY1
triangles) and
S
942 to WY2012).
pawning Success Opportunit
y (SSO) da
ys (blue squares) modele
d
58 for Lower
F
p
igure 34. Low Ri
precipitation exce
sk Spawning (L
R
edence (WY1942
S) da
ys (red tria
n
to WY2012).
ngles) and Spaw
ning Success Opportunit
y (SSO) days (blue squares) modeled for El Ja
59 ro Creek vs
F
v
igure 35. Low Ri
vs precipitation e
x
sk Spawning (L
R
xceedence (WY194
S) da
ys (red tria
n
42 to WY2012).
ngles) and Spawning Success Opportunit
y (SSO) da
ys (blue squares)
modeled for Los
A
60 moles Creek
61 4.6 Annual Low Risk Spawning Day Findings
Model results indicated that a tributary’s potential to offer abundant LRS days was highly variable but also highly dependent on annual precipitation. Ordering water years by exceedence probability (P) on the X-axis revealed a clear relationship to Annual Low Risk Spawning Days at all three Salsipuedes Creek spawning destinations (Figure 33, Figure 34, and Figure 35). For spawning destinations higher in the watershed and located in smaller tributary watersheds, there were many fewer LRS days. As watershed area and streamflow decreased, the annual total of LRS days also decreased. For the Lower Salsipuedes Creek spawning destination (Figure 33), LRS days were abundant in WYs with P values ranging from 1% to 35% and common up to approximately 65%. For the El Jaro Creek spawning destination (Figure 34), LRS days were abundant in WYs with P values ranging from 1% to 25% and common up to approximately 45%.

For the Los Amoles Creek spawning destination (Figure 35), LRS days were abundant from 1% to 10% and then common up to only 35%. There were qualitative differences as well among the three destinations. The presence of continuous LRS vertical bars in Lower Salsipuedes Creek continued up to P values of 25%, up to 10% for El Jaro Creek, and never occurred in the Los Amoles Creek spawning destination. The long, unbroken LRS bars indicated overlapping storms with sufficient receding streamflows to continue providing abundant spawning habitat and qualifying as a LRS day (i.e., the redd incubation streamflow threshold was not limiting). Wetter years may not be better because they are wetter, but because the odds of having closely-spaced floods with overlapping storm recession limbs increase sharply. Figures 30 to 32 clearly showed by the many gaps, given all WYs from WY1942 to WY2012, that some years had very few or no LRS days even in Lower Salsipuedes Creek.

4.7 Annual Successful Spawning Opportunity Day Findings The first Lagoon breaching event established ‘opening day’ of the adult steelhead spawning season (i.e., the first day that an adult steelhead could enter the Lagoon and SYR mainstem from the Pacific Ocean). After the breach of the Lagoon, there is an inevitable minimum delay time of 3 to 3.5 days until the steelhead adults could arrive at the mouth of Salsipuedes Creek (i.e., the time it takes for an adult steelhead to travel from the Lagoon to the mouth of Salsipuedes Creek under rapid migration conditions). Once adult steelhead were in the mainstem of the Santa Ynez 62 River, subsequent storms (even minor ones, especially if two or more overlapped one another by 4 to 6 days) could have adults staged at the confluence, ready to enter Salsipuedes Creek when the next storm flows eventually arrived (i.e., no delay for the second flood event) and cued upstream migration.

Lower Salsipuedes Creek was accessible to spawning adult steelhead during the Gibraltar Dam and Cachuma/Bradbury Dam periods. Long and continuous vertical bars of SSO days for some WYs were generally associated with wet years. WY1983 and WY1998 had two of the longest, complete bands; their respective P values were 4.3% and 1.1% qualifying both as Extremely Wet water years. In contrast there were notable gaps (e.g., late-1940’s to early-1950’s, late-1980’s to early-1990’s) during protracted droughts. A prominent outlier was WY1942 (P = 65.5%) that had just the right combination of small floods not frequently encountered in drier years that was also preceded by an Extremely Wet water year (demonstrating that there can be ‘hydrologic memory’ from one water year to the next). At a broader temporal scale, the 1950s and 1960s offered few success opportunities.

4.8 Assessing Potential Effects of Adult Steelhead Migration Delay on Successful Spawning Opportunity Days in Salsipuedes Creek The Salsipuedes Creek watershed has a flashy runoff pattern where daily average streamflows have reached 503 cfs with an instantaneous peak of 1,430 cfs (record from March 15, 2003) at USGS Gaging Station No. 11132500 Salsipuedes Creek near Lompoc but then dropped to a daily average streamflow of 40 cfs one day later (March 16, 2003). LRS days mostly occurred on and immediately after storm peaks. Examining a single storm event and starting from the mouth of Salsipuedes Creek, the model showed adult steelhead generally migrated to headwater spawning destinations within two days or missed the peak event altogether. Missing the peak event would mean that the steelhead would not arrive on a LRS day, if it arrived at all. If migration from the mouth of Salsipuedes Creek to the Los Amoles Creek spawning destination took more than four days, adults missed the LRS days created by that storm event. This occurred because receding storm flows quickly dropped below the model’s spawning habitat streamflow threshold (5 cfs for the Los Amoles Creek spawning destination). Adult steelhead likely could locate spawning habitat at lower streamflows, but the threshold was meant to target higher quality and reasonably 63 abundant spawning habitat. At very low streamflows, redds must be constructed very close to the channel’s thalweg in pool tails. During scouring floods, these redds incur a high risk of being scoured-out. A season of field data could quantitatively identify the streamflow scour threshold.

Minimal delay from the Santa Ynez Lagoon to the mouth of Salsipuedes Creek was estimated between 3 and 4 days (using a maximum 5 mi/day daily average migration rate). Perhaps under ideal hydrologic conditions a 10/mi day migration rate would have made this a 2-day delay.

From the mouth of Salsipuedes Creek up to El Jaro Creek and Los Amoles Creek the minimal modeled delay was 1 to 2 days, thus making minimal migration delay from the Santa Ynez Lagoon up to the El Jaro Creek spawning destination 4 to 5 days. By understanding and quantifying this effect of migration delay in the Salsipuedes Creek watershed, we could better understand the implications of delay attributable to the mainstem (e.g., through reduced streamflows, and therefore lower migration rates).

In a season with multiple storms in close succession, the delay factor may account for only a few missed LRS days. However, for single storm events the delay factor may have meant no LRS days were counted as SSO days. WY2008 at the El Jaro spawning destination was analyzed to explore this reduced delay effect. The entire WY2008 migration season was assessed, followed by assessments for individual storm events.

The WY2008 hydrograph (Figure 36) had several peak events during the migration season. Daily average streamflows were converted into RCT depths using a USGS Stage-Q rating curve in Lower Salsipuedes Creek (before USGS constructed a weir) converted to an RCT-Q rating curve. An annual riffle depth-o-graph was generated for Lower Salsipuedes Creek (Figure 37).

An immediate impression from Figure 37 was the brevity during which the WY2008 migration season has riffles flowing deeper than an adult steelhead. The time window for achieving SSO days higher into Salsipuedes Watershed lasted only a few days per storm before RCT depths dropped below 0.4 ft deep (Figure 38). Even at 0.4 ft, adult steelhead can still maneuver upstream, though the risk of encountering complete blockage becomes considerably greater.

Figure 38 illustrated why the quickly rising and falling streamflows limit migration successes as the water depth at the RCT falls below the fish's back, leaving the migrating steelhead with its 64 back partially out of water. While RCT depths less than the depth of the steelhead may not halt upstream migration in the model, migration rates were sharply reduced. Figure 39 shows the miles traveled, starting at the mouth of Salsipuedes Creek for each day of the migration season, up to the spawning destination in El Jaro Creek, as well as the river miles traveled each storm event. Note that steep lines indicated greater distances traveled in one day, whereas horizontal lines indicated streamflows dropped to the point where migration effectively stalled. When migrating into the watershed on the falling limb of a storm hydrograph, reduced migration rates compounded the days required to reach the spawning destination, if the spawning destination could have been reached at all.

Figure 36. Hydrograph of Lower Salsipuedes Creek (WY2008). 12/15 1/15 2/15 3/15 4/15
0 50
100
150
200
250
300
350
400
Date
Flow (cfs)
Lower Salsipuedes Creek
Figure 37
scale.
. WY2008 hydrograph converted to Riffle Crest Thalweg Depth with an adult steelhead fo 65 r size
Figure 38. The WY2008 hydrograph converted to daily RCT depths at each spawning destination. Streambed and adult steelhead drawing for scale comparison. 66 Figure 39
date for W
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for upwar
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1 1
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. Hydrograph
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69 4.9 Sensitivity Analysis Modeled for Daily Average Migration Rate Daily average migration rate was an important model parameter. The ratio of total annual SSO Days / total annual LRS days measured how well a given WY performed at the specified spawning destination in a given WY. A ratio close to 1 meant that most LRS days could have been utilized by migrating adult steelhead. If daily average migration rates were a primary factor affecting this outcome, a change in daily average migration rates should change the ratio in many WYs. Los Amoles Creek should be affected more than the other destinations because it had a narrower window of spawning opportunity given its small drainage area. Baseline daily average migration rates (Figure 29) were used to compute this ratio over the complete Lower Salsipuedes Creek USGS gaging record. For WYs ranging from P values of 1 % (i.e., an Extremely Wet WY Type) to approximately 30% (i.e., a Wet WY Type), the ratio remained above approximately

0.85 in Lower Salsipuedes Creek, between 0.90 and 0.80 in El Jaro Creek, and between 0.80 and

0.60 in Los Amoles Creek (Figure 42). When the baseline daily average migration rates (for each RCT depth) were increased by 25% (Figure 43), the respective ratios remained approximately the same. When the baseline daily average migration rates were decreased 25% (Figure 44), the ratio noticeably dropped for El Jaro Creek and Los Amoles Creek. Therefore, if actual migration rates are faster (i.e., our baseline migration rates are under-estimating), we would not expect a major increase in SSO days (i.e., the ‘true’ ratio changes little from our modeled predictions), but if actual migration rates are slower, we would expect a considerable decrease in the total annual SSO days (i.e., the ‘true’ ratio would drop considerably from our modeled predictions, especially for Los Amoles Creek).
70 Figure 42. Ratio of Total Annual Successful Spawning Opportunity (SSO) Day / Total Annual Low Risk Spawning (LRS) Days by Total Annual Precipitation Exceedence using baseline daily average migration rates for WY1942 to the present.

Figure 43. Ratio of Total Annual Successful Spawning Opportunity (SSO) Day / Total Annual Low Risk Spawning (LRS) Days by Total Annual Precipitation Exceedence using daily average migration rates 25% greater than baseline rates for WY1942 to the present.
0 20 40 60 80 100
0 0.2

0.4 0.6

0.8 1
Total Annual Precipitation Exceedence(P, %)
Annual SSO Days/ Annual LRS
Days
Baseline Daily Average Migration Rates
Lower Salsipuedes Creek
El Jaro Creek
Los Amoles Creek
0 20 40 60 80 100
0 0.2

0.4 0.6

0.8 1
Total Annual Precipitation Exceedence(P, %)
Annual SSO Days/ Annual
LRS Days
Daily Average Migration Rates
Increased 25%
Lower Salsipuedes Creek
El Jaro Creek
Los Amoles Creek
71 Figure 44. Ratio of Total Annual Successful Spawning Opportunity Days / Total Annual Low Risk Spawning Days by Total Annual Precipitation Exceedence (P, %) using daily average migrations rates 25% less than baseline rates for WY1942 to the present.

4.10 Conclusions
A watershed as large as Salsipuedes Creek (and as close to SYR Lagoon), with its smaller tributary watersheds, can provide low risk spawning days even in Below Normal WYs that spawning adult steelhead can utilize provided they do not experience major delays along their migration route. Modeling indicated that migrating adult steelhead during the Bradbury Dam Period have been able to utilize low risk spawning days in Lower Salsipuedes Creek, but less so in the upper watershed’s tributary Los Amoles Creek.

Minimal delay from SYR Lagoon to the mouth of Salsipuedes Creek is between 3 to 4 days (possibly 2 days). From the mouth of Salsipuedes Creek upstream to El Jaro Creek and Los Amoles Creek the minimal delay is an additional 1 or 2 days. Making the minimal overall delay from SYR Lagoon to the spawning destination in El Jaro Creek a minimum total of approximately 5 days. Salsipuedes Creek storm hydrographs are flashy. Adult steelhead migration into the upper watershed generally can occur only during a storm event or immediately 0 20 40 60 80 100
0 0.2

0.4 0.6

0.8 1
Annual SSO Days/ Annual LRS
Total Annual Precipitation Exceedence (P, %)
Days
Daily Average Migration Rates
Decreased by 25%
Lower Salsipuedes Creek
El Jaro Creek
Los Amoles Creek
72 thereafter. For an isolated storm event with an adult staged at the mouth of Salsipuedes Creek, the model shows either fish migrating to spawning destinations within one to two days, or the fish misses the peak event in which case migration takes considerably more time. If migration takes more than 4 to 5 days, the fish will often have arrived after available LRS days have ceased (too shallow). Thus the likelihood of a delay effect (attributable to streamflows in the SYR mainstem) will highly depend on whether, or not, adult steelhead are poised at the mouth of the tributary and can take immediate advantage of the next flood peak. Even a seemingly minor SYR Lagoon breach, early in a typical migration season with short-lived mainstem migration flows, can begin a slower upstream journey under minimum passage flows to tributary confluences that will greatly reduce delay effects come the next storm event (i.e., improve chances that fertilized eggs will be deposited in the upper regions of the watershed). Shapovalov likely was witnessing this in 1946 (an Abv-Normal WY) as adult steelhead were “moving upstream” near Alisal Creek confluence on March 28-29 (Titus et al. 2006). On March 28, 1946 the streamflow was 22 cfs near San Lucas Bridge; on March 29, 1946 the daily average streamflow rose to 226 cfs signaling an approaching storm event (USGS Water Supply Paper No.1061). 73 5 Steelhead Juvenile and Smolt Outmigration

5.1 Introduction
San Lucas Bridge is the ‘Gateway’ to the Santa Ynez River floodplain. This Gateway not only marked a physical transition from headwaters to valley-bottom floodplains, but a pivotal change in steelhead life history strategy. Downstream migrating smolts, pre-smolts, and juveniles passing under San Lucas Bridge, in spring and early-summer, would soon enter a productive aquatic environment existing in an otherwise arid landscape. Although their individual odds for success still remained slim, especially so for the YOY steelhead, they could continue growing on their journey downstream. In somewhat of a paradox, viability of the historic Santa Ynez’s steelhead population may have hinged on there being a big reservoir. Only this reservoir was the river’s underground aquifer.

This chapter evaluates how changes in the annual hydrograph below the San Lucas Bridge Gateway affected juvenile steelhead outmigration. The following steps to achieving this end were: (1) document changes in summer baseflows during the Gibraltar Dam and Cachuma/Bradbury Dam Regulatory periods relative to the Pre-Gibraltar Dam Period, (2) define ‘connectivity’ and develop streamflow thresholds quantifying it, and (3) measure connectivity for juvenile steelhead outmigrating from Salsipuedes Creek during Contemporary Bradbury Dam annual hydrographs .

5.2 Spring and Summer Baseflows from San Lucas Bridge to Lompoc Substantial summer baseflows in the Pre-Gibraltar Dam-Period annual hydrographs (Figure 5) are missing in the Contemporary Bradbury-Dam Period annual hydrographs (Figure 6). Summer baseflows were plotted by annual precipitation exceedence to quantify the relationship between summer streamflows and water year type. Pre-Gibraltar Dam summer baseflows at Lompoc and at San Lucas Bridge were plotted for mid-June (Figure 45) mid-July (Figure 46) and mid-August (Figure 47). The labels ‘mid-June’ or ‘mid-July’ were necessary, rather than stating a given date, because many miscellaneous streamflow measurements were not taken daily. Therefore, streamflows measured on June 10 and June 18 were collectively applied in preparing these plots to take advantage of the limited, early-1900s gaging data. 74 Lower bound curves (sometimes called ‘envelope curves’) were plotted to establish a lower streamflow magnitude at any given P-value. There were no confidence intervals or statistical tests involved, so fitting lower bound curves could introduce bias. Whenever a lower bound line was used in the analysis, the original plotted data from which the line was made were included.

The lower bound line establishes a minimum hydrological response to P while emphasizing natural interannual streamflow variability.

Figure 45.
lower bou
Pre-Gibralta
nd curves.
r Dam Period mid-June summer baseflow at Lompoc and San Lucas Bridge with 75 Figure 46.
lower bou
Pre-Gibralta
nd curves.
r Dam Period mid-July summer baseflow at Lompoc and San Lucas Bridge with 76 Figure 47.
lower bou
Pre-Gibralta
nd curves.
r Dam Period mid-August summer baseflow at Lompoc and San Lucas Bridge w 77 ith
78 For WYs close to the average annual precipitation (P = 38%), the Lompoc summer baseflows went from a lower bound of 38 cfs in mid-June, to 17 cfs by mid-July, and remained about the same in mid-August. Lower bound baseflows exhibited a remarkable stability over a wide range of P-values. In mid-June (Figure 45) lower-bound summer baseflows remained similar between approximately 20% and 50% P-values. For a watershed with low annual rainfall, this lent stability to a river ecosystem in an arid landscape that steelhead could utilize as an important destination point for steelhead at certain times of the year and life stages.

In selected years, the difference in streamflow between San Lucas Bridge and Lompoc could exceed 40 cfs. In mid-July, this difference in WY1915 was 53 cfs (Figure 46). WYs that plotted well above the lower bound line, such as WY1915, could result from numerous reasons, including unseasonal summer rain. The peak flow of 32,500 cfs on February 9, 1915 never receding below 1000 cfs until early-March, kept streamflows high through the summer of WY1915 (USGS Water Supply Paper No. 411, p. 111). Variability in streamflow magnitude over a narrow range of P-values for Lompoc decreased into the summer, suggesting an increasing dominance of groundwater over surface streamflows.

Summer baseflows at San Lucas Bridge exhibited a completely different trend. By mid-July, baseflows were only a few cfs in WYs with P-values greater than 30% or even 20%. The transition from almost no summer baseflow to 10 cfs or greater was sharp at approximately P = 15% throughout the summer. Summer baseflow variability was low, suggesting San Lucas Bridge was a predictably poor destination for steelhead most of the summer except in deep thermally stratified pools.

With intensifying groundwater demands in the Santa Ynez Valley and several new dams, summer baseflows at Lompoc were vulnerable. Similar to the Pre-Gibraltar Dam plots of summer baseflow and P-values, additional plots were made of Lompoc summer baseflows during the Gibraltar Dam Period for June 15 (Figure 48) and Cachuma/Bradbury Dam Period for June 15 (Figure 49). Figure 50 summarizes the 3 lower bound curves that includes the PreGibraltar Dam Period.

F
F
igure 48. Upper igure 49. Upper
and lower bound and lower bound
lines for June 15 slines for June 15 s
ummer baseflowummer baseflow
s near Lompoc dus near Lompoc du
ring the Gibralta
uring the Bradbur
ar Dam Period.
ry Dam Period.
79 F
D
igure 50. Compa
Dam Period near
rison of lower bo
Lompoc.
und lines for mi
d-June summer baseflows during Pre-Gibraltar Da
m Period, Gibraltar Dam Period, a
n
80 d Bradbur
y
81 Summer baseflows in the Lower Santa Ynez River were being severely impacted by the 1920s and 1930’s. A P-value of 60% (a Dry WY) had a lower bound streamflow of 30 cfs at Lompoc in the 1910’s but essentially 0 lower bound streamflows 20 to 30 years later during the Gibraltar Dam Period. In wetter WYs the trend continued. By P = 20% (a Wet WY), lower bound streamflows during Bradbury Dam Period were approximately 2 cfs (Figure 50). The loss of stable summer baseflows over a wide range of annual precipitation exceedences must have had a strong negative effect on juvenile steelhead residing in the Lower Santa Ynez River, after migrating from the headwaters above San Lucas Bridge. This life history tactic for YOY juveniles required lower mainstem streamflows that extended into summer.

5.3 Lompoc/San Lucas Bridge Summer Streamflow Ratio
Another way to portray summer baseflows in the Lower Santa Ynez River (i.e., below San Lucas Bridge), was a ratio of daily average streamflows, Q Lompoc/Q SanLucasBridge, to illustrate the relative dominance of groundwater accretion in the Lower Santa Ynez River before Gibraltar Dam operations and intensive groundwater pumping began (Figure 51). Beginning mid-June or earlier, and before Gibraltar Dam in WY1920, streamflows in the upper watershed (above San Lucas Bridge) and in downstream tributaries (e.g., Salsipuedes Creek) dropped-off sharply. But not far downstream from San Lucas Bridge, groundwater accretion compensated for these disappearing surface streamflows. A few small downstream tributaries were spring-driven. Santa Cota Creek near Solvang flowed at 6 cfs to 8 cfs throughout most of the summers of WY1914 (P = 10.4 %) and WY1915 (P = 28.2 %) (from miscellaneous streamflow measurements in USGS Water Supply Paper No. 721).

Figure 51. Ratio of daily average streamflows, Q Lompoc/Q SanLucasBridge, during late-spring and summer for pre-Gibraltar Dam annual hydrographs. 82 83

5.4 Channel Connectivity

5.4.1 Introduction
As streamflows naturally declined from early-spring (March 1) into late-summer (September 1), steelhead smolts, pre-smolts, and juveniles encountered different aquatic environments during their passage downstream that might last a few weeks, or over a year. Channel connectivity was maintained when successive channel segments along a juvenile steelhead’s downstream migration route continued offering the opportunity to migrate freely and to grow significantly while migrating. Dam operations, groundwater pumping, and surface diversions on the Santa Ynez River, by changing spring and summer hydrographs, have affected how well tributary and mainstem channels maintain connectivity for steelhead outmigration.

Salsipuedes Creek has the greatest natural potential for producing smolts and juveniles below Bradbury Dam. Salsipuedes Creek watershed will need to contribute disproportionately to smolt production, directly raising smolts inside its watershed boundaries, but also contributing indirectly by supplying juvenile steelhead to the Lompoc mainstem, and then the Santa Ynez Estuary, to grow into smolts. Connectivity between Lower Salsipuedes Creek and through the Lompoc Floodplain to the Santa Ynez Estuary will be vital to steelhead recovery. Two threshold streamflows to help measure connectivity were investigated: (1) CDFG’s juvenile steelhead minimum passage streamflows (CDFG 2012), and (2) minimum channel connectivity streamflows.

5.4.2 Juvenile Steelhead Minimum Passage Depth and Streamflow CDFG (2012) requires minimum depth criteria for evaluating downstream passage of young-ofthe-year (0+) and 1+/2+ juvenile steelhead. For young-of-the-year (0+) steelhead, the minimum passage depth is 0.3 ft; For 1+ and 2+ juvenile steelhead, the minimum depth is 0.4 ft (CDFG 2012). As discussed for adult steelhead passage, these minimum depth criteria establish the minimum acceptable depth on both boundaries of the 10% contiguous corridor (i.e., the bookend depths) along a riffle’s cross-section using CDFG’s application of the Thompson Method (Thompson 1972). Many depths, if not most, between the bookend minimums will be deeper assuming the 10% continuous corridor includes the thalweg. To adapt RCT depths to the 84 Thompson Method criteria, the following RCT depth thresholds were used to estimate a minimum juvenile steelhead downstream passage streamflow from a RCT-Q rating curve: (1) minimum RCT depth = 0.4 ft for 0+ juvenile steelhead and (2) minimum RCT depth = 0.5 ft for 1+/2+ juvenile steelhead. Both RCT minimum depths, each 0.1 ft deeper than the CDFG required minimum depths, accommodate a gentle transverse riffle slope such that the bookend depths of the 10% Thompson Method contiguous corridor width approximated CDFG’s minimum depth. For Lower Salsipuedes Creek, a RCT depth of 0.50 ft required QJuvMinPass = 5.6 cfs; for mainstem Santa Ynez River at ‘H’ Street near Lompoc, a RCT depth of 0.50 ft required QJuvMinPass = 9.9 cfs.

5.4.3 Tributary and Mainstem Channel Connectivity
As spring/summer streamflows gradually decline below juvenile steelhead minimum passage streamflows, core riffle areas retract until streamflows through the riffles start to severely restrict most biotic interchange between adjoining runs and pools. This restricted biotic interchange includes: (1) juvenile fish physically (contacting the bed surface) navigating through riffles (to avoid poor water quality and/or exchanging disappearing habitat in one run or pool for another) while exposed to greatly elevated stress and risk and (2) a sharp reduction in benthic macroinvertebrate (BMI) drift and productive riffle bed surface area supplying prey to juvenile fish in downstream pools and runs. ‘Disconnection’ begins when streamflow drops below the minimum connectivity streamflow. In Mediterranean river ecosystems, tributary and mainstem disconnection is a natural process with its own duration, frequency, and timing of occurrence.

For the mainstem SYR, an RCT depth of 0.25 ft was the minimum depth selected for channel connectivity. When applied in the field, this minimum depth would be represented by the median RCT depth taken from a large sample of RCTs. Consequently, streamflows that provide the minimum RCT depth will vary considerably. When estimated in the office (less preferable), the streamflow providing the minimum 0.25 ft RCT depth was estimated from a RCT-Q rating curve converted from a USGS Q-Stage rating curve. For Lower Salsipuedes Creek, an RCT depth of

0.15 ft was our minimum. This minimum was less than that for the mainstem primarily due to the mainstem’s much greater channel width and propensity toward seepage through wide alluvial riffles. An RCT depth of 0.25 ft at ‘H’ Street nr Lompoc required QMinConnect = 2.7 cfs; an RCT depth of 0.15 ft on Lower Salsipuedes Creek required QMinConnect = 1.0 cfs. 85 Downstream migrating smolts/juvenile steelhead in Salsipuedes Creek were often captured when declining streamflows in April and May approached 3 cfs (2008 Biological Monitoring Report, US Bureau Reclamation 2011), which is equivalent to a 0.20 ft RCT depth. Kelley (2008) found that the greater portion of the smolt run in Salsipuedes Creek during WY2008 out-migrated between March 29 and April 15. USGS Gaging Sta. No. 11132500 Salsipuedes Creek nr Lompoc recorded declining daily streamflows between 5.3 cfs and 3.2 cfs during this time period, equivalent to an RCT depth range of 0.28 ft to 0.22 ft.

5.4.4 Assessing Connectivity between Lower Salsipuedes Creek and the Mainstem Santa Ynez River near Lompoc
The litmus test for connectivity was a contrast between QMinConnect = 1.0 cfs for Lower Salsipuedes Creek (LSC) and QMinConnect = 2.7 cfs for the mainstem SYR at ‘H’ Street. If the date for when QMinConnect occurred at ‘H’ Street was later than the date QMinConnect occurred at LSC, this would be supportive evidence for channel connectivity. If the date for QMinConnect in LSC was the same date for QMinConnect on ‘H’ Street, then both channels were closing-down juvenile steelhead migration at approximately the same time. This scenario was labeled ‘minimum connectivity’ and would not be a desirable environment for juveniles migrating out of Salsipuedes Creek. But if QMinConnect at ‘H’ Street occurred before QMinConnect on LSC, connectivity was being compromised (i.e., disconnection) in some fashion. Some juveniles emigrating from LSC would find the mainstem a barrier to migration. The greater the negative difference in days, the greater the likelihood of disconnection effects.

Large negative differences (measured in days) between the two dates by WY in Table 3 indicated poor overall connectivity during the Contemporary Bradbury Dam Period. These results also were presented graphically (Figure 52). Juveniles emigrating from Lower Salsipuedes Creek are encountering poor migration conditions, and likely poor growth/survival, upon entering the LSYR mainstem.

86 Table 3. Comparison of QMinConnect of Salsipuedes Creek and Santa Ynez Rive at H Street among WYs during Contemporary Bradbury Dam Period (‘>Sept 01’ means streamflows exceeded the QMinConnect past Sept 01; ‘<March 01’ means QMinConnect occurred prior to March 01).

WY
P-values
(%)
WY
QMinConnect for
Lower Salsipuedes
Creek
(1.0 cfs)
QMinConnect for
Santa Ynez River
at H Street
(2.7 cfs)
Difference
(days)

25.8 WY2000 >Sept 01 June 09 - 83

14.0 WY2001 >Sept 01 June 16 - 76

97.8 WY2002 May 12 March 16 - 57

37.6 WY2003 June 26 May 22 - 35

90.3 WY2004 April 27 <March 01 - 58

2.2 WY2005 >Sept 01 July 14 - 48

26.9 WY2006 >Sept 01 June 24 - 68
100.0 WY2007 April 26 March 07 - 50

28.0 WY2008 June 17 April 24 - 54

83.9 WY2009 April 20 March 16 - 35

23.7 WY2010 June 17 May 10 - 38

16.1 WY2011 >Sept 01 July 09 - 53

91.4 WY2012 May 03 May 01 - 2
100.0 WY2013 April 02 DRY ALL YEAR NA
Figure 52
QMinConnect
Under th
water yea
would ha
connectiv
Lompoc
mainstem
juveniles

2. Minimum c
for the mains
he Pre-Gibra
ar with the s
ave been a
vity on June
Floodplain
m with a hi
s encountered
connectivity l
stem Santa Yn
altar Dam P
ame P value
minimum o
e 17, 2008 j
during the P
gh growth
d the Lompo
line for QMinC
nez River at ‘H
Period, the l
e as WY2008
of 40 cfs.
juvenile stee
Pre-Gibraltar
potential wh
oc Floodplai
Connect = 1.0 cf
H’ Street = 2.7
ower bound
8 (P = 28%,
Until Lowe
elhead emig
r Dam Perio
hile migrati
in disconnec
fs in Lower
7 cfs.
d, mid-June
a borderline
er Salsipued
grating from
od would ha
ing (i.e., hig
cting on Apri
Salsipuedes C
streamflow
e Wet to Abo
des Creek re
m Salsipuede
ave encounte
ghly connec
il 24, 2008 a
Creek (Y-axis
at Lompoc
ove Normal
eached mini
es Creek int
ered a produ
cted). Emigr
at 2.7 cfs.
87 s) and
c in a
WY)
imum
to the
uctive
rating
88 Lost connectivity was most clearly shown by the juvenile steelhead monitoring data, rather than indirectly through examining the timing of streamflow thresholds. In the 2008 Monitoring Report (US Bureau Reclamation 2011), juvenile steelhead captured outmigrating from Lower Salsipuedes Creek were leaving primarily throughout April (in the 2008 Monitoring Report:

Figure 34 (b), p. 80). Most of the potential smolts were 160 mm to 190 mm long (in the 2008 Monitoring Report: Figure 35, p.81). But on May 3, 2008 the mainstem SYR streamflow at ‘H’ Street had dropped to 0 cfs.

Successful downstream juvenile migration required more than meeting the connectivity threshold. Shapovalov (1944) documented millions of steelhead fry were in the mainstem, or leaving tributaries and heading to the mainstem, by late-Spring. These fry emerging in March through early-May had to grow rapidly on their downstream journey to have any chance of survival. A mainstem channel providing sufficient flow depth for 50 mm to 70 mm long fry to swim downstream (i.e., the minimum connectivity streamflow) could not provide the necessary nurturing environment necessary for rapid growth. Another threshold was identified and quantified to address this need. Minimum passage streamflow thresholds for yearling juveniles and 1+ juvenile/smolts, both based on minimum riffle crest thalweg depths tied-back to CDFG’s Thompson protocols, were estimated for the mainstem and Salsipuedes Creek. Receding spring streamflows beginning at these minimum passage streamflows, then transitioning to the minimum connectivity streamflow, would create retracting riffles, with much of their surface areas diminished with streamflows confined along the thalweg.

Although the magnitude, duration, and timing of each WY’s spring recession streamflows were unique, they all shared a common transformation heading into summer. Beginning mid- to lateMarch, SYR mainstem riffles were often still wide and hydraulically complex, creating productive habitat conditions for benthic macro-invertebrates (BMI). As smolts and pre-smolts migrated downstream, high riffle BMI productivity greatly increased opportunities to feed and therefore grow. Greater growth meant increased ocean survival, improving the odds of returning to the SYR as an adult to spawn. Depending on initial size upon entering the SYR mainstem, a 5% increase in fork length while in the mainstem could improve survival odds measurably. For YOY’s, productive riffles offered refuge from predation, ample food, and habitat space. With 89 millions of YOY soon swamping the mainstem, to escape shrinking tributary channels and the upper LSYR mainstem, space may have been the most important commodity, not minimum flow depths through riffles.

5.5 A Lompoc Streamflow Seepage Threshold for a Dry ‘H’ Street Channelbed Currently, the Santa Ynez River mainstem passing Lompoc remains dry most summers.

Although several factors are involved, seepage loss can readily be identified as one. By noting the first day that the daily average streamflow dropped to 0 cfs at the USGS gaging station at ‘H’ Street nr Lompoc, an estimate of seepage loss was made by looking-up the daily average streamflow, for the same day, measured by the USGS above Robinson Bridge (Figures 1 and 2) shortly upstream. Since the 1930s, seepage loss has increased steadily (Figure 53). The lead-up to the mainstem going dry at ‘H’ Street broadcasts no warning in the streamflow record. Instead, daily average streamflows at ‘H’ Street and above Robinson Bridge (whether measured at the ‘Narrows nr Lompoc’ USGS station or ‘nr Lompoc’ USGS station) uniformly tracked one another until the ‘H’ Street streamflow simply ‘bottomed-out’ at 0 cfs (Figure 54 and Figure 55).

Figure 53.

Narrows n
Ynez River
Threshold st
r Lompoc’ or
r at ‘H’ Street
reamflow at e
‘nr Lompoc’
nr Lompoc fir
either Lompoc
’) on same day
rst reported a
c USGS gaging
y downstream
0 cfs daily av
g stations (dep
m USGS Gagin
verage streamf
pending on wa
ng Station No.
flow.
ater year: ‘at
. 11134000 San
90 ta
Figure 54.
31, 2000 to
Figure 55.
to May 27
. Parallel rece
o June 16, 200
. Parallel rece
7, 1962.
ession limbs o

00. ession limbs of
f daily averag
daily average
ge streamflow
e streamflows
s at ‘H’ Stree
s at ‘H’ Street
t and at the N
and at the Na
arrows from
arrows from M
91 m May
May 7
92 The USGS ‘H’ Street gaging station has had an uneven history of continuous streamflow measurement. In some WYs only spot measurements were made. At first, these miscellaneous measurements were not considered useful because we could not be certain of the first day that streamflow at ‘H’ Street hit 0 cfs. However, after plotting the upstream and downstream station data on one graph, we realized that a seepage estimate could be made (simply subtract the daily streamflows for several days of parallel streamflows and average them) because of the uniform tracking between hydrographs (Figure 54 and Figure 55). The two ways of computing seepage loss were distinguished in Figure 53.

In the early to mid-1930s, seepage loss averaged approximately 2.2 cfs. By the mid-1950’s it was 6 cfs, and by the early-2000’s it was 9 cfs. The WY2000 to WY2011‘spaghetti’ plot of annual hydrographs (Figure 56) revealed how much loss of mainstem connectivity has been happening.

The ‘Normal’ water year (in light green) intersecting 5 cfs on June 8 would have gone dry at ‘H’ Street at 2.2 cfs or approximately July 12th in the early-1930s. But by the mid-2000’s the date had been advanced to approximately May 28th (using a 9 cfs seepage loss). Notice that the Dry/Critically Dry years, as well as Extremely Wet and Wet years, have steeper summer recession streamflows (Figure 56). A steeper slope meant there would be less forward advancement of the ‘H’ Street mainstem channel losing connectivity, and eventually drying-up.

However, a critical period for many migrating juvenile steelhead would be in late-spring. As tributaries rapidly approach their connectivity streamflow thresholds, many juvenile steelhead must escape to the mainstem Santa Ynez River.

F
Streamflow (cfs)
igure 56. Annual hydrographs from WY1990’s and WY2000’s at Lompoc for spring a Date
nd summer baseflows less than 20 cfs.
93 94
The pair of Dry years intersecting 5 cfs between April 20 to 25 (Figure 56) once went dry in early-May of the 1930’s (assuming the same streamflows occurred then as in the spaghetti graph (likely they were greater then)), but now go dry around April 10. Steelhead smolts generally migrate early, with March and April prime months. Many Salsipuedes Creek smolts must be finding the mainstem Santa Ynez River disconnected with no option but to remain in the mainstem until marginal connectivity resumes. With so few smolts in the system, and few 0+ juveniles present as well, pre-mature loss of channel connectivity must be addressed in even Dry water years. When Shapovalov (1944) reported rescuing 26,000 juvenile steelhead from Alisal Creek between May 26 and June 20, WY1940 was a borderline Below Normal - Dry water year (P = 68.8%).

In the Pre-Gibraltar Dam Period, connectivity was assured in Dry WY’s through July and at least August. Unfortunately from WY1908 to WY1918 USGS gaging encountered only one drier water year, WY1913 with a P = 67.8% making it a borderline Below Normal – Dry water year type. Measured streamflows at USGS Gaging Station nr Lompoc measured in September of WY1913 exceeded the minimum passage streamflow for ‘H’ Street. Downstream migrating juvenile steelhead could still swim to the SYR Estuary through summer. This was likely the norm in all but the driest WYs. Extended connectivity may have been unusual among other large SoCal rivers. The SYR mainstem, closely confined by terraces, is only 200 ft to 400 ft wide throughout most of the Lompoc Floodplain. A narrow, incised mainstem meandering through a broad floodplain with a healthy groundwater table could sustain low surface streamflows well into summer. But much wider rivers, such as the Santa Clara River and Santa Maria River, might not.

The sharp increase in loss between 1940 and 1960 was observed by Evenson (1966) who noted:
“Subsurface inflow, or underflow of ground water, through The Narrows into the Lompoc subarea is determined by the cross-sectional area, the permeability of the saturated deposits, and the hydraulic gradient. The saturated cross-sectional area did not change appreciably during the inventory period, the permeability is a constant, but the hydraulic gradient varied during the period of inventory. For the period 1935-44 the ground-water levels were high, and an average hydraulic gradient of 8 feet per mile resulted in an average underflow of 600 95 acre-feet per year (Upson and Thomasson 1951, p.80). However, as the use of ground water in the Lompoc subarea has increased, the water levels were lowered in heavily pumped areas downstream from The Narrows, and the hydraulic gradient through The Narrows has steepened. Thus, for the period 1947-51, the gradient averaged 20 feet per mile, and the annual underflow averaged 1,500 acre-feet (Wilson 1959, p.83). The hydraulic gradient for the period of this study is similar to that for 1947-51; hence, the estimated subsurface inflow was about the same, or an average of 1,500 acre-feet per year.”

5.6 Preliminary Assessment of Juvenile Steelhead Growth in the Mainstem Lower Santa Ynez River and Its Importance to Recovery
Juvenile steelhead leaving Salsipuedes Creek need to encounter favorable growth conditions in the mainstem channel to significantly improve their chance of returning to spawn. This potential improvement was assessed preliminarily by modeling daily growth under very basic assumptions and scenarios. A smolt-to-adult-return curve (SAR curve) can be used to estimate the increase in smolt-to-adult return as a function of steelhead length, thus quantitatively connecting increased growth with increased survival. With most juvenile steelhead rearing habitat behind Bradbury Dam (SYRTAC 2000), and the Lower Santa Ynez River mainstem impacted by excessive groundwater withdrawal, providing better mainstem habitat quality for longer duration, and therefore better stream productivity and juvenile growth, is the most viable restoration strategy.

An important management objective is how far to the right (i.e., increased duration) in Figure 58 should the dotted line be extended via real-time flow releases. One cfs released for 24 hours requires approximately 2 ac-ft, therefore knowing how much steelhead recovery benefit could be derived from springtime releases would be essential.

This preliminary, simplified assessment relied on a range of daily juvenile steelhead growth rates that could apply to the Lower Mainstem Santa Ynez River. Hayes et al. (2008) found a 0.08% per day estuarine growth rate. This would be very high for a typical headwater tributary, even the trunk channel segment of a large tributary. A 0.5% per day growth rate would be optimistic as well. But the mainstem channel is not a headwater tributary. We modeled juvenile steelhead 96 growth (with the dependent variable being fork length) using constant daily growth rates of

0.2%, 0.3%, and 0.5% per day.

Two life history tactics were targeted: steelhead fry entering the mainstem in their first spring and small to large steelhead 1+ juveniles entering the mainstem in their second spring. Initial steelhead lengths modeled were: 45, 70, 90, 110, 120, 140, 150, 160, and 170 mm. Duration also determines juvenile length gains at each growth rate for each initial length. Therefore durations of 20, 40, 60, 80, 100, and 120 days were modeled (Tables 4 through 6).

Table 4. Lengths of juvenile steelhead using a 0.2% per day constant growth rate.

Number
of Days
Start
size
45 mm
Start
size
70 mm
Start
size
90 mm
Start
size
110
mm
Start
size
120
mm
Start
size
140
mm
Start
size
150
mm
Start
size
160
mm
Start
size
170
mm
20 46.7 72.7 93.5 114.3 124.6 145.4 155.8 166.2 176.6
40 48.6 75.7 97.3 118.9 129.7 151.3 162.2 173.0 183.8
60 50.6 78.8 101.3 123.8 135.0 157.5 168.8 180.0 191.3
80 52.7 82.0 105.4 128.8 140.5 163.9 175.6 187.4 199.1
100 54.8 85.3 109.7 134.1 146.2 170.6 182.8 195.0 207.2 120 57.1 88.8 114.2 139.5 152.2 177.6 190.3 202.9 215.6 Table 5. Lengths of juvenile steelhead using a 0.3% per day constant growth rate.

Number
of Days
Start
size
45 mm
Start
size
70 mm
Start
size
90 mm
Start
size
110
mm
Start
size
120
mm
Start
size
140
mm
Start
size
150
mm
Start
size
160
mm
Start
size
170
mm
20 47.6 74.1 95.3 116.4 127.0 148.2 158.8 169.4 180.0
40 50.6 78.7 101.2 123.6 134.9 157.3 168.6 179.8 191.1
60 53.7 83.5 107.4 131.3 143.2 167.1 179.0 190.9 202.9
80 57.0 88.7 114.0 139.4 152.0 177.4 190.0 202.7 215.4
100 60.5 94.2 121.1 148.0 161.4 188.3 201.8 215.2 228.7 120 64.3 100.0 128.5 157.1 171.4 200.0 214.2 228.5 242.8

97 Table 6. Lengths of juvenile steelhead using a 0.5% per day constant growth rate.

Number
of Days
Start
size
45 mm
Start
size
70 mm
Start
size
90 mm
Start
size
110
mm
Start
size
120
mm
Start
size
140
mm
Start
size
150
mm
Start
size
160
mm
Start
size
170
mm
20 49.5 77.0 98.9 120.9 131.9 153.9 164.9 175.9 186.9
40 54.7 85.0 109.3 133.6 145.8 170.1 182.2 194.4 206.5
60 60.4 93.9 120.8 147.6 161.1 187.9 201.3 214.7 228.2
80 66.7 103.8 133.5 163.1 178.0 207.6 222.4 237.3 252.1 100 73.7 114.7 147.5 180.2 196.6 229.4 245.8 262.2 278.5 120 81.5 126.7 162.9 199.1 217.2 253.4 271.6 289.7 307.8 140 90.0 140.0 180.0 220.0 240.0 280.0 300.0 320.0 340.0

5.7 Estimating Improved Smolt Survival from Springtime Bradbury Dam Releases in the Lower Santa Ynez River Mainstem
Many factors specific to the water year and Pacific Ocean conditions shape the smolt-to-adultreturn relationship (SAR) between adult return and smolt length. Therefore, applications of a general SAR curve for predicting adult steelhead return must be interpreted broadly. We used an SAR curve utilized in an instream flow study of Alameda Creek for the SFPUC by McBain and Trush (2012, p.11). The equation that best fit this SAR curve for steelhead smolts between 130 mm and 190 mm is 2E-26*(smolt length in mm)^10.703.

This preliminary analysis explores the possibilities/feasibilities that improved baseflow releases as juveniles migrate downstream would make a highly significant contribution to recovery. For example, the Salsipuedes Creek 140 mm smolt entering the Pacific Ocean experiencing no additional growth in the mainstem or estuary would have a 0.19% return. But if this juvenile grew to 160 mm in the mainstem and/or estuary, its chance of return would increase to 0.78%: a

0.78/0.19*100 = 411% improvement. We selected two life history tactics as simple examples for how this approach/strategy could develop.

Steelhead Life History Tactic No.1. A 140 mm juvenile leaves Salsipuedes Creek on April 1 (i.e., having over-wintered in Salsipuedes Creek) then remains in the mainstem for 2 months under unusually favorable streamflows (for occurring during Cachuma/Bradbury Regulatory Period) encouraging good growth. Without additional growth before entering the Pacific Ocean its SAR = 0.19%. By growing under good conditions (using 0.5% per day growth rate) in the mainstem

4.35%, o
improvem
Steelhead
redd on
period of
and then
until mid
estuary a
be extrem
(Table 3)
evaluate
50 mm.

Figure 57.

The histo
good star
(REF) ob
m for 2 mont
or a 4.35/0.
ment would
d Life Histo
March 1, e
f 40 days thi
remain in th
d-June befor
at 45 mm FL
mely low). If
) would still
(in October)
. Smolt-to-Adu
oric mainste
rt (fish alrea
bserved mov
ths (60 days
.19*100 = 2
still be a 647
ory Tactic N
enters the m
s means the
he mainstem
e entering th
L, its SAR w
f the fry rem
l be too low
) the advanta
ult Return Cu
em channel w
ady 70 mm
ving through
) it grows to
2289% imp
7% improve
No.2. A steel
mainstem on
eggs from it
m under good
he estuary. W
would be too
mained until
w to estimate
age of a 0+
urve from McB
would have
and maybe
h the SYR m
o 187.9 mm
rovement. W
ement.
lhead fry em
March 15
ts redd were
d growth con
Without addi
low to estim
June 15 (90
e as well. H
entering the
Bain and Trus
primed gro
larger) for t
mainstem in t
(from Table
With a 0.3%
merges from
(with a con
e fertilized ap
nditions (of
ditional grow
mate from Fi
0 days), its S
However, a s
e estuary at 8
sh (2012, p.11
owth in the S
the millions
the 1940’s. M
e 3), and its
% per day
m a Lower S
nservatively
pproximately
streamflow
wth, swimmin
igure 57 (i.e
SAR at appro
simple next
80 mm or 70
).

SYR Estuar
of 0+ steelh
Moore (1980
SAR increas
growth rate
alsipuedes C
short incub
y on Februar
and tempera
ng directly t
e., survival w
oximately 70
step would
0 mm, rather
ry by provid
head Shapov
0, p.74) note
98 ses to
e, the
Creek
bation
ry 1),
ature)
to the
would
0 mm
be to
r than
ding a
valov
es for
99 the Ventura River that: “Though the amount of rearing habitat in the main stem of the river is quite limited, it proved to be highly productive. Rapid growth rates were observed during the study under summer and fall base flow conditions. This growth occurred in response to generally favorable habitat conditions which were the result of stable base flow augmented by rising groundwater, warm (though not limiting) water temperatures, water quality conducive to rapid growth (800 – 1000 micromhos/cm at base flow), an abundance of food organisms, and a prolonged growing season.” With warmer water into summer (even if originating from local groundwater), micro-crustaceans would have been the late-season prey of choice – a formulae for high productivity and growth. Moore (1980, p.61) concludes: “Table 14 compares the mean fork length of 0+ and 1+ steelhead reared in the study area with steelhead from four more northerly Pacific Coast streams with generally lower average water temperatures (modified from Cross, 1975). A comparison of these growth rates indicates that steelhead reared in the Venture River obtain smolt size (~ 15+cm) in the first year of stream life, rather than the second or third year as do most steelhead from more northerly streams.” If the Pre-Gibraltar mainstem SYR below San Lucas Bridge was as productive as some contemporary estuaries are today (e.g.,

0.8% per day juvenile steelhead growth rate; Hayes et al. 2008), life history tactics growing 0+ smolts could have been highly successful at sustaining large annual adult steelhead runs.

100
6 Channel Hydraulics in the Lower Santa Ynez River and Its Importance to Steelhead Migration, Life History Needs, and Recovery

6.1 Introduction
From one life stage to the next, stream hydraulics are center-stage in creating abundant, highquality steelhead habitat in the Lower Santa Ynez River. What can be considered ‘good’ streamflows for steelhead fry rearing during outmigration or ‘good’ streamflows for adult steelhead migrating upstream to spawn will entirely depend on how the particle size, slope, woody riparian vegetation, and channel configuration of each river segment interacts with the variable streamflow of annual hydrographs. Fisheries biologists frequently need to measure the fish habitat resulting from these physical interactions. PHABSIM (Physical Habitat Simulation) seeks to establish a quantitative relationship between streamflow and each life stage’s habitat abundance by skipping-over the characterization and quantification of channel hydraulics. At first this strategy seems preferable. Why attempt to quantify the highly complex world of river channel hydraulics as a precursor to establishing each life stage’s habitat – streamflow rating curve, when these curves can be measured/modeled directly. We argue otherwise. Stream hydraulics are complex. But considerable quantifiable insight can be derived by adopting a generalized hydraulic perspective for predicting habitat – streamflow relationships. This was particularly valuable for re-evaluating instream flows in the Lower Santa Ynez River because the 2000 BiOp had to rely on limited data/analyses for establishing quantifiable habitat – streamflow relationships and thresholds.

The available science was constraining with one notable exception. A DWR PHABSIM Study investigated instream flows from Bradbury Dam downstream 13.6 miles to Buellton (Denton 1989). However, the DWR Study was rejected by the newly-formed SYRTAC in 1993, with SYRTAC (1997, Job No.3) subsequently planning to engage another instream flow study without indicating whether it would extend through the Lompoc Floodplain. No parallel PHABSIM instream flow investigation was, or has since, been attempted farther downstream, thus omitting 23.9 miles of additional mainstem channel downstream to the Santa Ynez River Estuary.
101
As discussed, an important (and arguably the most important) role of the Lower Santa Ynez River mainstem was, and is, to grow juveniles and smolts along their way downstream from latewinter through late-spring, and into summer as annual streamflows and water temperatures allow or are mitigated. Natural tributary inflow from tributaries below Bradbury Dam cannot sustain productive, or even sufficient, mainstem streamflows capable of providing good juvenile growth in many water years. Therefore, a quantitative understanding of the magnitude of streamflows capable of providing good juvenile and smolt rearing/migration habitat will be necessary to define the tasks ahead for steelhead recovery. The purpose of this section was to use river channel hydraulics, in lieu of directly measuring habitat abundance and quality, for identifying streamflows capable of providing good steelhead fry, 1+ juvenile, and smolt rearing habitat, including adult steelhead spawning habitat as well, throughout the Lower Santa Ynez River mainstem.

6.2 Background
Our river channel hydraulic investigation relied on USGS gaging station stage-Q rating curves. A rating curve’s shape is a function of stream hydraulics. Streamflow gaging requires an awareness to pronounced and subtle changes in stream hydraulics. Braca (2008) describes how hydraulic controls influence stage-Q rating curves typically constructed at USGS gaging stations such as those within the Santa Ynez River Basin (Figure 58):
“The stage-discharge relation for open-channel flow at a gauging station is governed by channel conditions downstream from the gauge. Knowledge of the channel features that control the stage-discharge relation [i.e., our study’s ‘Stage-Q rating curve] is therefore a crucial component in developing rating curves. Three types of controls can be recognized, depending on the channel and flow conditions:
 low flows are usually influenced by a section control;  high flows are usually influenced by a channel control  medium flows can be influenced by both type of controls.

At some stages, in fact, a combination of section and channel control can occur. 102
A section control is a specific cross-section of a stream channel, located downstream from a water level gauge that controls the relation between gauge height and discharge at the gauge. A section control can be a natural feature such as a rock ledge, a sand bar, a severe constriction in the channel, or an accumulation of debris. Likewise, a section control can be a man-made feature such as a small dam, a weir, a flume, or an overflow spillway. Section controls can frequently be visually identified in the field by observing a riffle, i.e. pronounced drop in the water surface, as the flow passes over the control. Frequently, as gauge height increases because of higher flows, the section control will become submerged in such a way that it no longer controls the relation between gauge height and discharge. At this point, the riffle is no longer observable, and flow is then regulated either by another section control farther downstream or by the hydraulic geometry and roughness of the channel downstream (i.e., channel control).

A channel control consists of a combination of features throughout a reach downstream from a gauge. These features include channel size, shape, curvature, slope, and roughness. The length of channel reach that controls a stage-discharge relation can be extremely variable. The stagedischarge relation for relatively steep channels may be controlled by a relatively short channel reach, whereas the relation for a relatively flat channel may be controlled by a much longer channel reach. In addition, the length of a channel control will vary depending on the magnitude of flow. The definition of the length of a channel-control reach is usually very difficult and it could be done, for example, by numerical methods.

At some stages, the stage-discharge relation may be governed by a combination of section and channel controls. This usually occurs for a short range in stage between section-controlled and channel-controlled segments of the rating (Figure 3). The development of stage-discharge curves where more than one control is effective or where control features change or where the number of measurements is limited, usually requires wide knowledge about the behavior of watercourse, in order to make a reliable interpolation between measurements and extrapolation beyond the lowest or highest measurements. This is particularly true where the controls are not permanent and tend to shift from time to time, resulting in changes in the positioning of segments of the stage-dis
both effec
Figure 58.

Braca (20
is the sta
height of
point in
sometime
control s
[this was
effective
heights o
straight l
to as the
Braca’s
immediat
specifica
scharge rela
ctive, is com
. Primary hyd
008) also no
age at gaugi
f zero flow (
the control
es be measu
section, and
s how the R
gauge heigh
of the disch
line. This is
e logarithmic
‘deepest pla
tely downstr
ally how US
tion. The pa
mmonly know
draulic control
otes: “One of
ing station c
(GZF). The r
cross-sectio
ured in the fi
subtracting
RCT-Q curve
ht of zero flo
arge measu
the reason w
c scale offse
ace in the co
ream of the
GS stage-Q
art of the ra
wn as the tran
ls for a genera
f the most sig
correspondin
real gauge h
on for a sec
field by meas
g this depth
es were con
ow is instead
urements, wi
why the effec
et.” In our h
ontrol sectio
gage plate.
rating curve
ting, where
nsition zone
alized stage-Q
gnificant fea
ng to the dis
height of zer
ction contro
suring the d
from the ga
nstructed for
d a value tha
ill cause the
ctive gauge h
hydraulic an
on’ is at the
RCTs are d
es were con
section con
.”
Q rating curve
atures in the
scharge clos
ro flow is th
ol. For natur
depth of flow
auge height
r assessing m
at, when sub
e logarithmi
height of zer
nalysis for th
thalweg dep
discussed in
nverted to RC
trol and cha
(from Braca 2
stage disch
se to zero, n
he gauge hei
ral channels
w at the deep
at the time
minimum fis
tracted from
ic rating cu
ro flow is so
he Lower Sa
pth of the r
n Report Sec
CT-Q rating
annel contro
2008).
arge relation
named the g
ight of the lo
s, this value
epest place i
e of measure
sh passage]
m the mean g
urve to plot
ometimes ref
anta Ynez R
riffle crest (R
ctions 3.4 to
g curves. Ge
103
ol are
nship
gauge
owest
e can
in the
ement
. The
gauge
as a
ferred
River,
RCT)
o 3.6,
eneral
104
shape and identifiable breakpoints in RCT-Q rating curves were associated with the physical habitat preferences of each steelhead life stage to recommend instream flows.

6.3 Constructing RCT‐Q Rating Curves for the Lower Santa Ynez River Mainstem Channel
The first step was to locate stage-Q rating curves at relevant USGS gaging stations. The morphology of the Lower Santa Ynez River mainstem changes from San Lucas Bridge to the SYR Lagoon. There has been little attention directed to assessing and managing Q-habitat relationships downstream of Robinson Bridge within the Lompoc Floodplain, even though this region could be a highly important bottleneck for basin-wide steelhead recovery. We centered our analysis on two locations near long-established USGS gaging stations, Solvang and Lompoc, to represent the steeper, narrower upper mainstem (Solvang) and considerably less steep, and wider, lower mainstem (Lompoc Floodplain). Beside the two targeted locations, additional USGS gaging station locations were investigated to better assess overall river change dating back to the Pre-Gibraltar Regulatory Period and compare hydraulic changes from the WY1969 flood.

Stage-Q rating curves were selected for their completeness (an issue primarily for earlier published rating curves): (1) number of points on the rating curve for Qave less than 6000 cfs, (2) points effectively spanning 0 cfs to 6000 cfs, and (3) a gage stage height preferably at 0 cfs or at least very close to 0 cfs. Most USGS Water Supply Papers (WSP) publications provided too few measures to accurately draft a complete rating curve from 0 cfs to 6000 cfs. Post-Water Supply Paper publishing only provides peak flood stages and a scattering of lower streamflow stages that could not be used to construct rating curves. However, a few earlier WSP rating curves were sufficiently complete to identify hydraulic thresholds.

The following RCT-Q rating curves were constructed from the USGS gaging record:

USGS Gaging Station No. 11123000 Santa Ynez River nr Santa Barbara WY1905 USGS Gaging Station No. 11123000 Santa Ynez River nr Santa Barbara WY1907-08 USGS Gaging Station No. 11128500 Santa Ynez River at Solvang WY2012 USGS G
USGS G
USGS G
USGS G
Pre-Gibr
curves. W
WY1907
(Figure 5
estimate
included
or even g
ft of stag
we subtra
curves (e

1.0 ft).

Figure 59.
aging Statio
aging Statio
aging Statio
aging Statio
altar reporti
We only use
7 and WY19
59) and WY1
hydraulic c
a point for s
greater. For p
ge down to 0
acted 1.70 ft
e.g., for WY
. Station ratin
n No. 11133
n No. 11133
n No. 11133
n No. 11134
ing by the U
ed two. A r
908 (the futu
1905 in WSP
ontrol stream
stage height
plotting an R
0 cfs (e.g., f
ft from each
Y1905, a gag
ng table reprod
3000 Santa Y
3500 Santa Y
3500 Santa Y
4000 Santa Y
USGS inclu
rating curves
ure site of G
P No. 177 pr
mflow thres
at 0 cfs, wit
RCT-Q curv
for WY1905
of the stage
ge stage heig
duced from U
Ynez River a
Ynez River n
Ynez River n
Ynez River a
ded selectiv
s for the Sa
Gibraltar Da
rovide suffic
holds (QT).
th 0.10 ft sta
ve from a rat
5, a gage hei
s (and their
ght of 2.70 f
SGS Water Su
at Narrows n
nr Lompoc W
nr Lompoc W
at ‘H’ Street
vely publish
anta Ynez R
am) publishe
cient detail t
Ideally, the
age increme
ting curve, w
ight of 1.70
correspondi
ft at 79 cfs w
upply Papers
nr Lompoc W
WY1967
WY1969
nr Lompoc
hing complet
River near S
ed in WSP N
to construct
e published r
ents at stream
we assigned
ft equaled 0
ing Q’s) to c
was assigned
No. 177 for W
WY2012
WY2012
te stage-Q r
Santa Barbar
No. 252 (p.

RCT-Q curv
rating curve
mflows to 20
an additiona
0 cfs). There
create the RC
d a RCT dep
WY1905.
105
rating
ra for
144)
ves to
e data
00 cfs
al 0.1
efore,
CT-Q
pth of
Stage-Q
USGS hy
bracketed
effect of
habitat. T
episodes
steelhead
Figure 60.
rating curv
ydrographer
d the major
pre-and pos
The Lower S
of woody r
d habitat and
. USGS Stageves nr Lomp
rs 9-210 rati
flood in lat
st-channel m
Santa Ynez R
riparian encr
d streamflow
-Q Rating Cur
poc for WY
ing table no
te-January o
morphologies
River will ex
roachment a
w will be chan
rve for ‘nr Lo
Y1967 and W
otes (Figures
of 1969, thu
s on hydraul
xperience m
nd equilibriu
nging contin
ompoc’ gaging
WY1969 we
s 60 and 61
us offering t
lic controls
more floods,
um. The lon
nually.
g station in WY
ere develop
). This pair
the opportun
and, ultimat
and subsequ
ng-term rela
Y1967.
ed directly
of rating cu
nity to asses
tely, on stee
uently exper
ationship bet
106
from
urves
ss the
lhead
rience
tween
Figure 61.

6.4 Ide
RC
Both hyd
Q rating
toward h
complex
for the L
defined s
control,
streamflo
(i.e., a re
. USGS Stageentifying
CT‐Q Ratin
draulic contr
curves. Low
higher stream
streambeds
ower Santa Y
streamflows
the line wa
ow); under t
elatively sm
-Q Rating Cur
Hydraulic
ng Curves
ols discusse
w streamflo
mflows incre
. This hydra
Ynez River
under gene
as steep (i.e
the influence
mall increase
rve for ‘nr Lo
c Controls
d by Braca (
ws transitio
easingly dom
aulic ‘transit
by fitting str
eral section a
e., a relativ
e of channe
in RCT dep
ompoc’ gaging
and Thre
(2008) were
oning from b
minated by
tion’ zone id
raight line se
and channel
vely great in
l control, th
pth per incr
g station in WY
esholds (Q
identified fr
being less d
channel con
dentified by
egments to o
l control. Un
ncrease in
he line had a
rease in stre
Y1969.

QT) in San
rom Lower S
dominated by
ntrol genera
Braca (200
our RCT-Q r
nder the infl
RCT depth
a distinctive
eamflow). Fr
nta Ynez R
Santa Ynez R
y section co
ates hydrauli
8) was estim
rating curve
fluence of se
per increa
ely shallow
rom Figure
107
River
RCTontrol
ically
mated
s that
ection
ase in
slope
58, a
108
straight line fit to the upper part of the rating curve, and another fit to the lower part of the rating curve, established an intermediate range of streamflows where the hydraulic control was ‘transitioning’ labeled ‘control breakpoints.’ For most rating curves, including Braca’s, a primary purpose in defining controls is for providing the best peak flow estimates for flood planning.

Thus the log scale on both axes, which unfortunately masks potential slope breaks among lower streamflows up to modestly high winter baseflows.

Using Figure 58 as a template, a refined characterization of streamflow ranges under different relative contributions of section and channel control (i.e., narrower than the 35 cfs to 250 cfs range in the Solvang RCT-Q rating curve) was made by locating all breakpoints on linearly plotted RCT-Q rating curves rather than plotted on log-scale. Threshold identification by identifying breakpoints (i.e., curve inflections) in RCT-Q rating curvature can be subjective. To minimize subjectivity, we drafted line segments onto each RCT-Q rating curve to totally define the curves as close as possible. A curve inflection was identified when two adjacent lines intersected at a sharp angle indicating an inflection point (Figure 62). The line-fitting reduced the bias but could not eliminate it. Consequently all RCT-Q rating curve worksheets (converted from stage-Q rating curves) with their drafted line segments were scanned (Figures 63 and 64). The strategy was to fit straight-line slope segments to each RCT-Q rating curve and identify streamflow thresholds (QT) at the breakpoints for section and channel controls, as well as to identify other controls and their streamflow thresholds.

Figure 62. Straight-line segments fit to contemporary ‘H’ Street RCT rating curve. 109
Figure 63.

Q (cfs) and
Scan of Solv
Yaxis=RCT
ang RCT-Q R
T Depth (ft) (N
ating Curve W
Note dual axes)
orksheet fo
.
or Identifying Hydraulic Breakpoints. (X
110
axis =
Figure 64.
= Q (cfs) a

6.5 Hy
The follo
A thresh
inflection
. Scan of ‘H’ S
and Yaxis=RC
ydraulic Co
owing hydrau
hold streamf
n) on each R
Street RCT-Q
CT Depth (ft) (
ontrols in
ulic controls
Section
Domina
Hydrau
Domina
Active
Domina
Channe
flow (QT) w
RCT-Q rating
Q Rating Curv
(Note dual axe
Santa Yne
s were identi
n Control
ant Section C
ulic Transitio
ant Active C
Channel Con
ant Channel
el Control
was estimate
g curve.
ve Worksheet
es).
ez River R
ified on each
Control
on Point
Channel Cont
ntrol
Control
ed for each
for Identifyin
CT‐Q Ratin
h RCT-Q rat
trol
h hydraulic
ng Hydraulic
ng Curves
ting curve ex
control’s b
Breakpoints (
s
xamined:
breakpoint (c
111
(Xaxis
urve
112
First, ‘active channel’ needs introduction. The active channel, as the name implies, is that part of the channel experiencing frequent scour and fine/coarse bedload transport (Armantrout 1998; Montgomery and MacDonald 2002), including entire riffle surfaces and flanks of point bars.

Often, its channel boundary is defined as the first line of permanent vegetation, although ‘permanent’ in alluvial channels can be difficult defining. The active channel is vulnerable to woody riparian encroachment if scour is significantly reduced in magnitude and frequency as often happens below dams. Looking off the Alisal Bridge, extensive woody riparian encroachment (permanent until the next very large flood) occupies the original active channel.

This has especially happened on oblique point bars, where encroached woody riparian vegetation now fundamentally alters channel hydraulics. In many mainstem locations, what would have been a broad oblique riffle are now narrow chutes (a lot easier mainstem channel setting for beavers building their dams).

In our investigation, Figure 58 changed Braca’s ‘Channel Control’ to ‘Active Channel Control’ and ‘Floodplain Control’ changed to ‘Channel Control.’ This, in turn, created two hydraulic transitions: from Section Control to Active Channel Control and from Active Channel Control to Channel Control. These changes considerably refined our hydraulic analysis by distinguishing narrow streamflow ranges relevant to specific habitat needs for several steelhead life stages. The hydraulic transition most directly relevant to generating steelhead rearing habitat was considered from Section Control to Active Channel Control.

The best way to explain these hydraulic controls and their respective QT’s is to begin at the Dominant Channel Control, which is located close to, or at, the maximum inflection for the entire (X-axis from 0 cfs to 6000 cfs), and then proceed to hydraulic thresholds at lower magnitude streamflows (Figure 65A and B). The Solvang RCT-Q rating curve will used as the example (Figure 65B). The other RCT-Q rating curves were assessed similarly to the Solvang and ‘H’ Street RCT-Q rating curves.

Figures 65
Controls a
B
A RCT Depth (ft) RCT Depth (ft)
5A and B. Co
and Threshold
ntemporary
(QT’s).
‘H’ Street (A) and Solvan
Ch
ng (B) RCT-Q
annel Discont
Channel Disco
Q Rating Cur
tinuity: 1.8 cfs
ontinuity: 2.7 c
rve with Hyd
fs
cfs
113
draulic
114
Hydraulic controls and thresholds (QT’s) for the Solvang RCT-Q rating curve were as follows:

QT = 550 cfs Dominant Channel Control means that channel control is becoming the dominant hydraulic influence at greater streamflows, with the hydraulic influence of the active channel beginning to wane. Therefore, ‘Dominant’ signifies transition. ‘Dominant Active Channel Control’ is the transition from dominantly Active Channel Control to primarily Channel Control.

Geomorphically, this signifies a transition is underway (from 550 cfs up to 2390 cfs) from the hydraulic roughness exerted by bedforms (e.g., broad riffles associated with oblique point bars) to the hydraulic roughness of the entire bankfull channel. As the rising stage at QT = 2390 cfs Channel Control approaches, many of these alluvial bedforms will be drowned-out (i.e., lose their relatively steep water surface slopes). Also, finer bedload transport and scour begins. For steelhead, QT = 550 cfs to 2390 cfs provides important, but indirect, habitat benefits, especially helping to prevent woody riparian encroachment (not scouring-out established plants, but vulnerable seedlings). Direct benefits include unimpeded adult migration (including less exposure to predation/people), but the downside includes an increasingly harsh environment for younger juveniles.

QT = 267 cfs Active Channel Control means the active channel is the hydraulic resistance affecting stage. Generally, riffle surfaces are entirely inundated though their margins might be just-inundated, with the central third or more experiencing higher velocities (> 2 ft/sec) promoting good benthic macro-invertebrate (BMI) riffle habitat. Tail-outs of pools and runs also are experiencing a wide range in depths and velocities that promote good adult steelhead spawning habitat. In long runs, a core of higher velocities (> 1.5 ft/sec) connects top and bottom.

QT = 124 cfs Dominant Active Channel Control means that a transition is underway, with active channel control beginning to dominate over section control. Most of the channel’s hydraulic responses to increasing active channel dominance are similar to those at Active Channel Control though to a lesser extent, within a given hydraulic unit (i.e., a pool, run, or riffle) and among hydraulic units. For example, the high velocity cores in many runs (particularly the broadest and longest) may not connect from the run’s top to the run’s bottom, whereas others will. In a SYRTAC

2.0 ft/sec
monitore
the High
Alisal Re
Figure 66
study reac
QT = 82 c
Active C
C (1999) inv
c in riffles o
ed was 50 cf
hway 154 R
each, but pos

6. SYRTAC (
ches of Lower
cfs Hydrauli
Channel Co
vestigation,
or 1.5 ft/sec
fs. But the sl
Reach) indica
ssibly only 7
1999) thalweg
Santa Ynez R
ic Transition
ontrol and
measured th
c in runs (F
lope of their
ated substan
75 cfs in the
g velocities as
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experiencing streamflows within the hydraulic transition zone beginning to transition to active channel control, offers a complex hydraulic environment. Successive mainstem pools, riffles, and runs will each have slightly unique, and occasionally very unique, hydraulic transition zone.

This uniqueness creates spatial complexity in mainstem steelhead habitats and productive BMI riffles at any given transition streamflow.

QT = 42 cfs Dominant Section Control is the RCT-Q rating curve’s inflection between 0 cfs and QT = 267 cfs Active Channel Control and locates where section control, as the dominant influence on channelbed hydraulics at lesser streamflows, has declined significantly.

QT = 8.5 cfs Section Control means the cross-section at the riffle crest is the hydraulic resistance affecting stage upstream (i.e., in the run or pool). Geomorphically, channel shape (up to the active channel stage) and particle size of the riffle crest are the determinant factors controlling depths and velocities upstream.

Comments:
(1) Pre-Gibraltar RCT-Q rating curves (Appendix) had similar QT’s even though both were located at the Pre-Gibraltar Dam Site and were not yet influenced by dams. The QT Dominant Section Control at the Gibraltar Dam Site (with a coarse alternating bar morphology) in WY1907-WY1908 was 45 cfs and 55 cfs in WY1905. QT Dominant Section Control estimates were slightly lower at Solvang (42 cfs) and ‘at Narrows nr Lompoc’ (43 cfs). With the distinctive wide, sandy mainstem channelbed below Robinson Bridge, we expected QT at ‘H’ Street to be even lower than it was (38 cfs). (2) In a WY1967 – WY1969 comparison of hydraulic control QT’s, mainstem channel morphology following the late-January 1969 flood had changed significantly: QT Active Channel Control in WY1967 was 450 cfs, but 1400 cfs in WY1969.

6.6 Influence of Hydraulic Controls on Steelhead Habitat Identification of hydraulic channel controls will be useful in the BiOp only if ecological significance can be ascribed to streamflow thresholds for each control. Habitat complexity, abundance, and quality are physical outcomes/byproducts of a hydraulically complex channel 117
(Statzner 1988; Ward 1989). Units for quantifying hydraulic complexity have not been formally established to our knowledge, but could include spatial variability in velocities, presence of eddies, diversity of vertical velocity profiles through pools, etc. All these hydraulic characteristics, among others, provide important habitat needs for aquatic flora and biota. The same channel segment may be hydraulically complex over one range of streamflows but not another. Section control, at 10 cfs or less in the Lower Santa Ynez River mainstem, generates relatively simple channel hydraulics and consequently offers limited habitat complexity to many species and their aquatic life-stages. Streamflows under the influence of section control in the Lower Santa Ynez River now occur throughout most summers and into many springtime periods even in wetter water years (Sections 5.2 and 5.3). By identifying the magnitude of streamflows influenced by various hydraulic controls, we could transform unimpaired and impaired annual hydrographs into annual hydraulic ‘complexity-o-graphs’ as one way to begin assessing changes in relative steelhead habitat abundance and quality since the early-1900s. A parallel change to the Lower Santa Ynez River, since significant flow regulation/diversion began in the early1920’s, has been a less conspicuous though steady change in low-flow active channel morphology primarily in response to woody riparian encroachment.

Our reliance on RCT-Q rating curves derived from the USGS stage-Q rating curves introduces a bias. USGS hydrographers choose sections of channel, for establishing their gaging stations, because these sites should be hydraulically well-behaved --- expected to produce simply shaped stage-Q rating curves (for accurate and precise daily streamflow estimates) with minimal expected shifts (and therefore, maintenance) in hydraulic control. Our use of these rating curves for assessing habitat quality and relative abundance was conservative. We expected to identify only an overall norm in RCT-Q curves, while not accounting for outlier RCT-Q rating curves (often associated with unique habitats). If a quantitative assessment of reach-wide RCT-Q variability is desired for the new BiOp, RCT-Q curve variability can be field-surveyed, at minor cost but with great accuracy, by measuring RCT depths (therefore, making an RCT-Q curve) in 10 to 15 hydraulic units (measured at their downstream riffle crest) near USGS gaging stations.

If carefully planned, and with a little luck, these curves can be constructed entirely from the recession limb of a single storm event.
118
QT Dominant Channel Control and QT Section Control mark two RCT-Q rating curve inflections, one nested within the other. The most interesting controls ecologically, and indicative of pronounced ecological change if one or more should change significantly (e.g., from woody riparian encroachment onto the active channel), are QT’s for the three ‘Dominant’ section, active channel, and channel controls. A simple inventory of channel controls would prove insightful regarding impacts to the river ecosystem broadly and to steelhead habitat specifically. This could be done by assigning each day of each annual hydrograph from the various regulatory periods to (1) streamflow below QT Dominant Section Control, (2) streamflows between QT Dominant Section Control and QT Dominant Active Channel Control, and (3) streamflows between QT Dominant Active Channel Control and QT Dominant Channel Control. There likely is a fourth ‘Dominant’ control not investigated: the transition from the bankfull channel to higher flood flows occupying floodplains and/or terraces (often revealed as distinctive breakpoints on gaging station rating curves). Highly desirable, from a steelhead direct habitat perspective, are the days with Qave’s between QT Dominant Section Control and QT Dominant Active Channel Control, when the channelbed undergoes a dominant shift in overall hydraulic behavior and, in the process, creates a highly complex channel for multiple steelhead life history stages. On most days of the water year, but particularly from late-winter through early-summer, the steelhead population relied on multiple habitat functions predictably performed by the Lower Santa Ynez River mainstem channel and its annual hydrographs.

6.7 Comparison of Solvang Mainstem Hydraulic Controls to DWR PHABSIM Study
The Lower Santa Ynez River PHABSIM study from 1987 to 1989 by CA Department of Water Resources modeled relative habitat abundance as a function of streamflow, using ‘weighted useable area’ (or WUAs), from Bradbury Dam downstream to Buellton (Denton 1989). Although WUAs are expressed in units of ft2, they too are not predicting actual habitat area. QT habitat thresholds predicted from our hydraulic analysis were compared to DWR’s PHABSIM study’s estimated WUA- Q rating curves for steelhead fry, juveniles, and spawning habitats from Bradbury Dam downstream to Buellton 13.6 miles downstream. 119
The original WUA-Q rating curve for Bradbury Dam downstream to Buellton (Denton 1989) extended to 160 cfs rather than the 140 cfs in Figure 67. Hydraulic controls estimated from the Solvang RCT–Q rating curve were superimposed for comparison. The asymptote of the fry WUA curve occurred close to QT = 42 cfs Dominant Section Control. With increasing streamflows, beginning at QT = 8.5 cfs Section Control, section control still dominated channel hydraulics but its dominance was declining. Streamflows beginning to exceed QT = 42 cfs Dominant Section Control were entering the Hydraulic Transition Zone, where section control lost its dominance. Steelhead fry prefer a shallow and slow moving channelbed typical when streamflows are dominated by section control. But fry WUAs remained relatively high through QT = 82 cfs Hydraulic Transition Zone, and still had not declined substantially up through QT = 124 cfs Dominant Active Channel Control. Unfortunately the DWR Study did not extend up through the next hydraulic control, QT = 267 cfs Active Channel Control. We expect steelhead fry WUAs to drop-off sharply between QT Dominant Active Control and QT Active Channel Control. Steelhead fry habitat remained relatively high over a considerable range in streamflows because different parts of the channelbed contributed at different streamflows. Below QT Dominant Section Control, open portions of the channelbed were shallow and sufficiently slow.

Above QT = 82 cfs, the open channelbed becomes too fast, thus shifting fry habitat toward the channel margins. In alluvial channels, the shallow margins can be expansive. This feature was extremely important in the Lower Santa Ynez River because more than one life stage occupied the mainstem on any day over most of the water year. The greatest uncertainty in associating hydraulic controls with fry (and juvenile) rearing habitat is the sensitivity of being impacted of riparian encroachment (occupying the margins of the active channel, encouraging deposition, and consequently narrowing the active channel). In Figure 65B note the narrow range in RCT depths (and therefore vulnerability to small changes) for QT’s within and below the Hydraulic Transition Zone: Dominant Active Channel Control (RCT depth = 1.47 ft) is only 0.42 ft deeper than QT Dominant Section (RCT depth = 1.05 ft).

F
f
igure 67. PHABS
from the contemp
IM WUA rating
orary Solvang RC
curves for steelhe
T-Q rating curve
ead fry refuge/rea
e.
ring, juvenile rearing, and adult spawning with superimposed hydra 120
ulic controls
121
Similarly, the asymptote for juvenile rearing WUAs occurred close to QT = 82 cfs Dominant Active Channel Control (Figure 67). Juvenile steelhead prefer faster and deeper streamflows.

Streamflows within the Hydraulic Transition Zone (42 cfs to 124 cfs) provide a hydraulically complex channelbed with faster and deeper hydraulic environments preferred by juveniles.

QT’s on the RCT–Q Contemporary Solvang Rating Curve (Figure 60) were closely associated with the shape of the Lower Santa Ynez River WUA-Q PHABSIM Curves (Figure 67). QT Hydraulic Transition equaled 82 cfs, where the Fry WUA-Q curve remained within a plateau of 800,000 ft2 to 900,000 ft2 and the Juvenile WUA-Q curve just approached its plateau of approximately 1,300,000 ft2
(Figure 67). This would be expected based on channel hydraulics.

The long runs and shallow pools of the Lower Santa Ynez River respond to section control with a relatively big increase in depth by adjusting (i.e., to accommodate higher streamflows) with only a small incremental increase in average velocity. This increase in RCT depth from QT Complete Section Control to QT Hydraulic Transition Point on the Solvang RCT-Q Rating Curve (Figure 65B) was 1.32 ft – 0.70 ft = 0.62 ft. An approximate 0.6 ft change in mainstem channel stage when under active channel control is an order of magnitude greater change in streamflow.

Adjusting with relatively small increases in velocity, over a shallow range in depth, will favor a hydraulic environment preferred by steelhead fry and small juveniles.

A significant limitation of the PHABSIM approach has been its near-complete reliance on preference criteria for depth, velocity, and substrate. In Figure 67, WUAs at 23 cfs and 100 cfs for steelhead fry are the same: 800,000 ft2
. This implies a dam release of 23 cfs or 100 cfs would produce the same ‘amount’ of habitat. Under most diversion scenarios, the 23 cfs instream flow release would always be recommended over the 100 cfs release (i.e., why release more water to accomplish the same outcome). The only prevalent exception has been water temperature. A release higher than 23 cfs might be recommended to achieve a given water temperature objective. But the two do not provide the same result even if water temperatures were not at issue. Unfortunately the units for WUA are square feet even though a WUA does not quantify actual channelbed surface area. The actual square feet of channelbed at 23 cfs will not be the same actual square feet of channelbed at 100 cfs. A long broad run in the Lower Santa Ynez River at 23 cfs, under Dominant Section Control, will be hydraulically simple. A run’s core 122
velocity (generally along the thalweg) will be less than 1 ft/sec or 0.5 ft/sec, with most of the run experiencing considerably slower velocities. The same long broad run at 100 cfs, now under a distinct mix of section and active channel controls, will be hydraulically complex. The run’s core velocity (generally along the thalweg) could be 1.5 ft/sec or 2.0 ft/sec, creating a diversity of feeding stations and encouraging benthic macro-invertebrate productivity. Much-improved riffle habitat increases the supply of prey to the run. The stage increase incorporates more of the low flow channel’s margins as fry habitat. Therefore, the WUA curve may show the ‘same’ habitat at 23 cfs and 100 cfs, but there would be a pronounced difference in habitat quality.

More than one steelhead life stage will be relying on mainstem Santa Ynez River runs/shallow pools on a given day. Over the winter, 0+, 1+, and 2+ juveniles will be rearing. By early-spring, pre-smolts and smolts will be growing their way downstream. Depending on when spawning occurs in winter, emergent fry from mainstem redds - and then from tributary redds - will be seeking mainstem refuge by early-spring: initially along the shallow margins for schooling but then into deeper and faster areas for rearing. Benthic macro-invertebrates in riffles will begin shifting from winter to a highly productive spring. All these simultaneous biological demands for habitat quantity and quality only can be met with a hydraulically complex mainstem channel. At Solvang, a 1.38 ft (RCT depth @ 100 cfs) – 0.83 ft (@ 23 cfs) = 0.55 ft increase in a run’s downstream RCT depth generates greater hydraulic complexity, in turn producing higher quality juvenile rearing habitat.

Results of the PHABSIM study (Denton 1989) were summarized as generalized WUA-Q rating curves (i.e., the product of assessing many transects for Q-habitat relationships to produce a single habitat rating curve), but individual transect data were not included. Depending on the perceived usefulness by NMFS of our hydraulic analysis for the upcoming BiOp, a request for, and analysis of, the field data might be warranted. Each set of transects provides a roughly independent estimate for habitat rating curve variability at different channel morphologies. If high quality photographs of these PHABSIM transects are available, then a field site relocation this fall would be useful. The DWR PHABSIM study followed the WY1969 flood that significantly reshaped (flattened and removed encroached woody riparian vegetation) channel morphology in the Lower Santa Ynez River mainstem by only 10 years. 123

6.8 Estimated Streamflow Ranges for Steelhead Life Stage Habitats We used our hydraulic QT’s to predict ranges of streamflow that should provide abundant and high quality habitat for: (1) steelhead fry rearing, (2) steelhead juvenile 1+ rearing, (3) steelhead smolt rearing/migration, (4) adult steelhead spawning above Solvang, and (5) BMI in riffles, and (6) BMI in runs at Solvang (Figure 68) and at ‘H’ Street (Figure 69). The key modifier ‘relative’ to all habitats acknowledges actual square feet of habitat could not be estimated from this hydraulic analysis.

Figure 68. Expected range of streamflows for each steelhead life stage’s physical habitat needs at Solvang in relation to hydraulic thresholds 124
.

F
h
igure 69. Expec
hydraulic thresho
ted range of strelds.
amflows for each steelhead life stage’s physical habitat needs at ‘H’ Street (Lompoc Floodplain) in 125
relation to
126
The lower portion of the Hydraulic Transition Zone (i.e., streamflows less than QT Hydraulic Transition Point) would be a favorable streamflow range (42 cfs to 82 cfs at Solvang and 38 cfs to 85 cfs at ‘H’ Street) for steelhead fry and yearling juveniles. The upper portion of the Hydraulic Transition Zone (i.e., streamflows greater than QT Hydraulic Transition Point) would be a favorable streamflow range (82 cfs to 124 cfs at Solvang and 85 cfs to 172 cfs at ‘H’ Street) for older steelhead juveniles, outmigrating smolts, and spawning adults in the Lower Santa Ynez River mainstem.
7 RECOMMENDATIONS
A Synthesis – “The Perfect Match”
The Santa Ynez River was a perfect match for Southern California steelhead. This perfect match began with the Santa Ynez River Basin being big, approximately 900 mi2. Only a big basin could provide the magnitude, duration, and frequency of daily riverflows that could meet the life history needs necessary to sustain a large steelhead population close to the species southern geographic limit. Infrequent, big floods rejuvenated the alluvial mainstem channel, built and rebuilt the floodplains, suppressed woody riparian encroachment, and maintained a dynamic balance between coarse sediment supply and deposition. Frequent, small floods kept pools deep, prevented broad riffles from aggrading with fine sediment, and likely were responsible for keeping the Santa Ynez Lagoon open longer during the year (because of their high frequency of occurrence relative to infrequent big floods). This geomorphic harmony of big and small floods with the alluvial SYR mainstem resulted in high quality, productive mainstem habitat for steelhead trout: deep scoured pools and broad riffles. Large volumes of winter and early-spring water flowing under San Lucas Bridge, the gateway between upper and lower SYR Basin, were stored in an annually rechargeable groundwater reservoir that supplied late-spring and summer streamflow to the Lower Santa Ynez River. Before the 1920s, a dry mainstem SYR channel at Lompoc in mid-August was a rarity (Figure 46). The Santa Ynez River mainstem below Solvang was a dependable biological hotspot for juvenile steelhead in an otherwise arid environment. 127
This 40-mile long hotspot for juvenile steelhead, including the Santa Ynez River Estuary, factored prominently in supporting two basic juvenile steelhead life history tactics deployed in the Santa Ynez River Basin: ‘to stay’ or ‘to leave.’ Both started out the same. Migrating adults passing through an open Santa Ynez Lagoon would strive to blanket as much of the Basin with their offspring (young-of-the-year (YOY)) as the hydrograph allowed. But then that year’s annual hydrograph, the luck of the parents’ draw, could exert additional limitations or opportunities. Would it be a dry or wet spring? YOYs born under this blanketing strategy would have more losers than winners even in a wet spring. Probably many more millions of YOYs left their natal origins in the tributaries and upper mainstem than stayed.

The ‘to leave’ life history strategy was not a conscious decision. As streamflows declined, habitat area contracted and habitat quality worsened sufficiently to force most YOYs to seek better quality habitat downstream. Timing was crucial. As vulnerable YOYs moved downstream (many having emerged from their mothers’ redds only 1.5 months previously), the mainstem had to offer a continuously connected migration route offering abundant and productive rearing habitat and minimal predatory risks while keeping the option open of continuing even farther downstream unimpeded. Otherwise, the migration route would become disconnected and the life history strategy ‘to leave’ within their first year would fail. In most years, the YOYs that survived to swim under San Lucas Bridge entered a radically new environment with unique challenges: could they rapidly grow in the lower mainstem and/or estuary until the following spring, or enter the Pacific Ocean before winter? The big Santa Ynez River Basin did supply the ‘to leave’ strategy its single-most critical ingredient as March transitioned into mid-May and early-June: predictable water.

The other prominent juvenile steelhead life history strategy was ‘to stay.’ Above San Lucas Bridge, streamflows in the SYR mainstem would gradually recede to a trickle even during before the 1920s (Figures 45 to 47) as its pools and long runs eventually disconnected from one another.

Juveniles that remained in the tributaries and upper mainstem channel would find refuge in deeper pools (especially in the higher elevation tributaries) and local coldwater mainstem refugia. The ‘to stay’ life history strategy was capable of producing smolts and pre-smolts over the coming winter. They then depended on favorable mainstem connectivity to freely migrate 128
and grow downstream the following spring along their entire migration route to the Pacific Ocean. Connectivity was a process that depended on the magnitude, duration, frequency, and timing of spring streamflows originating from gradually receding limbs of big floods, but even more so, from late-season small floods. A mid-May rainfall/runoff event could be invaluable in a drier water year to extending mainstem connectivity into summer.

Both steelhead life history tactics relied on annual connectivity, only at different life history stages. ‘To leave’ may have been by evolutionary design: emulating a life history strategy of Chinook salmon that avoids spending a summer in freshwater. For this strategy to succeed, the YOYs needed to grow, a lot, to survive in the mainstem and/or SYR estuary and then enter the Pacific Ocean before winter arrived.

The Santa Ynez River ecosystem met Aldo Leopold’s definition for health as “the capacity for self-renewal” (in his 1944 essay: Conservation: In Whole or in Part?). It was a perfect match for sustaining a large population close to the southern limits of the steelhead’s geographic range. But all the self-renewing ‘parts’ had to remain in working order.

Gibraltar Dam became operational in WY1920. It diverted late-spring and early-summer baseflows (mid-summer baseflows were naturally very low upstream), thus hastening tributary disconnection to the SYR mainstem from Gibraltar Dam downstream to the Santa Cruz Creek confluence, as well as disconnection within the SYR mainstem (as CDFG’s Leo Shapovalov observed in the early-1940s and attempted several years of juvenile (mostly YOYs) steelhead rescues. Gibraltar Dam also physically eliminated abundant, accessible prime spawning habitat and abundant ‘to stay’ anadromous juvenile rearing habitat from 219 mi2 of the Basin,
particularly within Mono Creek. Greater basin area had meant more YOYs to fuel the ‘to leave’ life history strategy that relied on huge numbers of YOYs because each had a very low chance of survival. And it did eliminate many smaller floods resulting in a 10% to 20% decline in reliable baseline passage opportunity days for adult steelhead migrating past Solvang in Below Normal WYs though less than a 5% loss in Wet water years (Figure 22). Losses at Lompoc were greater (Figure 23). But Gibraltar Reservoir’s low storage capacity and location high in the headwaters still left room for steelhead and people to coexist.
129
Bradbury Dam broke all the parts required to sustain a large steelhead population but one.

Overdrafting of the groundwater below San Lucas Bridge was rapidly compromising the Santa Ynez River’s biological hotspot before the drought, beginning in the late-1940s and early-1950s.

Cachuma Reservoir first filled in April WY1958. Overdrafting essentially eliminated the ‘to leave’ life history strategy because there wasn’t enough water for juveniles to grow through summer and into fall, and it greatly jeopardized the ‘to stay’ strategy by reducing a smolt’s opportunity to grow during migration. Reliable minimum mid-June baseflows near Lompoc for Above-Normal water years (P =30% to 50%) went from approximately 37 cfs in the PreGibraltar Dam Period (Figure 45) down to approximately 20 cfs in the Gibraltar Dam Period (Figure 48). During the Cachuma/Bradbury Dam Period, the decline in summer flow continued, with a reliable minimum mid-June baseflow of approximately 7 cfs (Figure 46).

Approximately 75% of all floods originating in the headwaters above San Lucas Bridge never reached the valley floor during the Contemporary Bradbury Dam Period (Figure 24). Only in the wettest years does Cachuma Reservoir spill floods. Consequently, the annual number of minimum reliable annual adult passage opportunity days at Solvang and Lompoc has dropped more than 80% or greater in Above Normal WYs (Figures 22 and 23). In the Contemporary Bradbury Dam Period, tributaries are expected to provide most streamflows of sufficient magnitude to allow upstream adult migration. But the storm hydrographs of the small tributaries below Bradbury Dam do not have, nor ever did have, the long recession limbs of the mainstem hydrographs originating from the upper watershed’s collective runoff. A silver lining accompanying these fewer reliable passage opportunities has been that adult steelhead need not travel as far to spawn with Bradbury Dam now blocking their way to the upper Basin. Below Bradbury Dam the watershed is narrow, with only the north-facing tributary watersheds sustaining adequate winter streamflows for adult steelhead to access low risk spawning habitat.

Lower SYR Basin tributaries (Figure 3) have the capacity to offer migrating adults high quality, low risk spawning days in most water years. Wetter years offered more low risk days than drier years. A clear outcome from modeling low risk spawning days (Section 4.6) was that the larger watersheds generated more low risk spawning days over a wider range of water year types (i.e., a wider range in P-values). For Lower Salsipuedes Creek at 47 mi2 , annual totals of low risk days
130
were high in Extremely Wet and Wet WYs (P-values 1% through 35%), substantial in Above Normal WYs (P-values from 30-50%), and sporadic in Below Normal WYs (P-values from 50- 70%) (Figure 33). For El Jaro Creek (21.1 mi2 and the major tributary of Salsipuedes Creek), low risk days were numerous in Extremely Wet and Wet WYs for P-Values of 1% through 25% (Figure 34). For Los Amoles Creek (4.3 mi2
and a tributary to El Jaro Creek, Figure 3), the
corresponding P-values were 1% to 10% (Figure 35). Therefore approximately 60% of the water years provided low risk spawning habitat in a watershed the size of Salsipuedes Creek.

Initially we expected steelhead spawning success in arid Southern California river ecosystems to have been historically limited to wet years that were typically separated by many drier years offering marginal or no spawning success. We reasoned that populations existing near their geographic limit should encounter extreme consequences. But our study indicated otherwise. The SYR steelhead population’s annual opportunity to successfully spawn would have been the norm, not the exception before groundwater pumping and surface water diversions. Construction of riffle depth-o-graphs at San Lucas Bridge from 70 estimated unimpaired annual hydrographs (Figure 70) showed that adult steelhead could have migrated up the mainstem channel during the three primary adult migration months (February, March, and April) in almost all years.

Without the magnitude and duration of the mainstem hydrographs, the window for migrating up tributaries always was much narrower and less forgiving. Over-lapping storm hydrographs were the surest way for adult spawners to access headwater tributaries (Figure 38).

F
c
igure 70. An ad
u
converted into an
n
lt steelhead’s size
ual riffle depth-o
contrasted with
-graphs from W
Y
dail
y average rif
Y1942 to the prese
fle crest thalweg d
ent. Water
year t
y
depth using esti
m
ypes are coded b
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ated annual h
y
dr
y color.
ographs at San
L
131
ucas Bridge
132
In addition to quantifying low risk spawning habitat capacity annually (measured in days), our model quantified potential utilization of this low risk spawning habitat capacity by estimating the total number of successful spawning opportunity days annually (Section 4.1). Our model quantified potential annual utilization of low risk spawning habitat capacity by estimating the total number of successful spawning opportunity days (Section 4.1). Use of the modifier ‘opportunity’ recognizes that the SYR’s depleted adult steelhead runs cannot take advantage because there are so few migrating adults participating.

With spawning habitat capacity and its potential utilization both measured in days, the ratio of successful spawning opportunity days / low risk spawning habitat days measured annual performance. A ratio of 1.0 signified every day that could have propagated successful redds could have been accessed by migrating adults. Above Bradbury Dam, this ratio will always be 0 for anadromous steelhead. For the Lower Salsipuedes Creek spawning destination (at the USGS gage), the ratio averaged 0.97 to 0.80 for Extremely Wet and Wet WYs, and then dropped to

0.80 to 0.65 for Above Normal and Below Normal WYs (Figure 42). Ratios for El Jaro Creek and Los Amoles spawning destinations were less, but still considerably above 50% (Figure 42).

These ratios were achieved even though the number of annual passage opportunity days through the Lompoc Floodplain have dropped since the Gibraltar Dam period (Figures 20 and 21).

Good spawning years in Wet and Above Normal WYs may produce many YOYs in a tributary watershed, but juveniles remaining in the watershed (betting on the ‘to stay’ strategy) for the upcoming summer, and then winter, will need favorable streamflows for outmigration connectivity the following spring. Of the 22 WYs since WY1990, sixteen were paired as a wet year followed by a dry year: WY1993 (P=9.7%) – WY1994 (P=54.8%), WY1995 (P=6.5%) – WY1996 (P=61.3%), WY1998 (P=1.1%) – WY1999 (P=75.3%), WY2001 (P=14.0%) – WY2002 (P=97.8%), WY2006 (P=26.9%) – WY2007 (P=100%), WY2008 (P=28.0%) – WY2009 (P=83.9%), and WY2011 (P=16.1%) – WY2012 (P=91.4%) (Table 1). Therefore, a successful spawning year will depend on that year’s spring outmigration streamflows (for the ‘to leave’ juvenile strategy) and the subsequent year’s outmigration streamflows (for the ‘to stay’ juvenile strategy). During the Contemporary Bradbury Dam Period, juvenile steelhead emigrating from lower Salsipuedes Creek have been disconnected from the Lompoc Floodplain 133
in 12 of 13 water years (Figure 52). The Lower Santa Ynez River has been drying-up prematurely since the early-1920s. In the early-1900s Pre-Gibraltar Dam Period, channel connectivity for tributaries downstream of San Lucas Bridge into mid-August was almost guaranteed in all but the driest years (Figure 47). Potential negative impacts incurred by a dry year that followed a wet year were buffered by summer groundwater accretion (Figures 45 (midJune), 46 (mid-July), and 47 (mid-August)).

One growing connectivity bottleneck has been the seepage loss of mainstem streamflows entering the Lompoc Floodplain. From the Narrows to ‘H’ Street near Lompoc, seepage losses have increased from 2 cfs in the 1920s to 9-11 cfs in the Contemporary Bradbury Dam Period (Figure 53). To maintain minimal connectivity at ‘H’ Street (estimated at 2.7 cfs), baseflows entering the Lompoc Floodplain must be at least 12 cfs (with 15 cfs a considerably safer threshold). The reliable minimum baseflow nr Lompoc for mid-June 15 was 10 cfs for a borderline Extremely-Wet / Wet WY during the Contemporary Bradbury Dam Period (Figure 50). In Figure 56, a horizontal dotted line at 10 cfs would represent 0 cfs at ‘H’ Street near the head of the Lompoc Floodplain and 4.9 miles downstream from USGS Gaging Station No. 11133000 Santa Ynez River at Narrows nr Lompoc (its annual hydrographs depicted in Figure 56).

When all parts of the Santa Ynez River Basin were working, the ‘to leave’ life history strategy could have produced the dominant share of returning adult steelhead over many years. Providing successful spawning opportunities without providing viable juvenile/smolt connectivity will stunt and likely prevent even marginal recovery. From the steelhead’s perspective, over-drafting of the floodplains’ groundwater reservoirs has been severe. Tributary streamflow accretion into the Lower Santa Ynez River mainstem cannot compensate for the groundwater loss (Figure 50).

Therefore, the policy of expecting the tributaries below Bradbury Dam to sustain adult spawning (being only partially successful, with Bradbury Dam spills contributing) cannot be extended to sustaining successful juvenile outmigration.
134

7.1 Recommendation No. 1. Think and Manage by Cohort Years not by Individual Water Years
Future management should consider pairing water years, as Cohort Years, to improve steelhead smolt abundance and adult run size. A Cohort Year (CY) would begin on SYR Lagoon’s opening day (signaling the start of the annual adult steelhead run) and end the following calendar year when spring recession streamflows can no longer grow and transport 1+ steelhead juveniles down the Lower Santa Ynez mainstem to the SYR Lagoon. For example, CY2008 would begin January 5, 2008 (predicted sand bar breaching) and end March 16, 2009 (when declining ‘H’ Street streamflows drop below the minimum connectivity threshold of 2.7 cfs). The end date could be extended to include 1+ juveniles leaving SYR Lagoon for the Pacific Ocean through their second summer, or possibly 2+ juveniles leaving the subsequent spring. Management actions would be under-taken to increase the length and quality of a CY. Each managed CY would broadly face three life history objectives: (1) good adult upstream migration, (2) good 0+ juvenile out-migration as smolts or reaching SYR Lagoon for additional growth, and (3) good 1+ juvenile/smolt outmigration the following spring.

The upshot for managing adult steelhead migration by cohort years is that we will not know if a given year’s migration season was ‘successful’ until the year afterwards. A great spawning year can produce abundant 1+ smolts the following spring only if recession flows that following spring are sufficient to promote smolt migration. As noted in the Synthesis, Dry-Wet WYs have been occurring in pairs between WY2000 and WY2012. If management treats the second year independently as a dry year incapable of contributing to recovery (e.g., scaling-back fish flow releases), then the recovery potential (i.e., lots of fertilized eggs to produce lots of smolts) of the previous water year’s good adult migration run will be jeopardized or worse negated. Only when two wet water years occur together would there be a realistic opportunity for success under this management scenario (e.g., possibly WY2010 (P = 23.7%) and WY2011 (P = 16.1 %)). This was not how the SYR Basin once sustained annual steelhead runs; instead, multiple generations of water management in the SYR Basin have made it that way. There are too few paired wet years to rely-on paired wet years as a viable population recovery strategy. 135
This concern can be explored one step further. Following a dry water year, a wet year’s early runoff frequently will be efficiently captured by a drawn-down reservoir. Early smaller storms would not pass Bradbury Dam and spring runoff could be reduced or eliminated, other than mandated minimal fish flows. One good cohort year, therefore, might require three successive wet years. From Table 1, there have been 5 sets of 3 consecutive wet water years each since 1900: WY1905-07, WY1914-16, WY1915-17, WY1916-18, and WY1991-93.

7.2 Adult Steelhead Migration Recommendation No. 2. Adult Steelhead Migration Real‐Time Bradbury Dam Releases

7.2.1 Introduction
The goal of annual steelhead runs has always been to blanket as much of the watershed with fertilized eggs as possible. To accomplish this challenging feat, adults need to get over the sandbar at the mouth, swim up the mainstem channel with minimal delay, enter and travel up the tributaries before streamflows become too low, build a redd and spawn, and then if very lucky, get back out. Most water years provided ample migration/spawning opportunities. Not just the wet years. Low risk spawning days for Lower Salsipuedes Creek and El Jaro Creek were predicted for water years with P-values approaching 70% (i.e., in DRY water years), though there was a drop in annual low risk spawning days above 35% (Figures 33 and 34).

Lake Cachuma Reservoir operations from WY1993 through WY2004 are summarized concisely in the SYRTAC Synthesis Report (2009, summary in Section 2.3.2). Contemporary management of steelhead migration relies on: (1) unimpaired tributary streamflows below Bradbury Dam to open, and keep open, SYR Lagoon as well as to prevent migration delay to the upper mainstem (above Solvang for relatively good spawning habitat) and to the tributaries, (2) Bradbury Dam spills, and (3) a Fish Passage Supplementation Program (summarized in Real-time Decision Group 2010). The Fish Supplementation Program was designed to shore-up this strategy caseby-case, while periods of Bradbury Dam spilling (once Lake Cachuma Reservoir fills) were considered sufficient in wetter years. Relying on our analysis, Figure 20 shows a sharp drop in Total Annual Adult Steelhead Passage Opportunity Days at ‘H’ Street during the CachumaBradbury Dam Regulatory Period. 136
An underlying management guideline has been that adult steelhead access and migration are needed primarily in wet years. Bradbury Dam eliminates a significant portion of basinwide winter streamflows that once provided many good migration days (not simply minimum passage days) and contributed to breaching the Lagoon, then keeping it open. Our report shows that the Santa Ynez River had the capacity to provide migration and spawning over a much broader range of water year types. The proposed alternative strategy relies on unimpaired streamflows from the Santa Ynez Basin upstream of Bradbury Dam to guide real-time management dam releases for adult steelhead migration below Bradbury Dam.

A Bradbury Dam release of 100 cfs from the watershed above Bradbury Dam was targeted on days when steelhead migration would have been encouraged before Bradbury Dam became operational. This relatively small contribution (unimpaired streamflows were considerably higher) would replace the present, implicit management strategy that the annual hydrograph generated by the Lower Santa Ynez River watershed (basically below San Lucas Bridge) sufficiently provides this life history function in most years.

A release strategy should avoid relying on predicting the WY Type (unlike in snowmelt dominated watersheds). This can be accomplished using real-time streamflows as the trigger for dam releases. It also should avoid, if possible, annually determining watershed “ground-water replenishment” in the tributaries before considering dam releases case-by-case. Even a brief storm (replenishment does affect storm hydrograph shape) can provide the opportunity to spawn successfully in the upper Lower Santa Ynez River mainstem or lower trunk of a large tributary (e.g., Lower Salsipuedes Creek). Without 100% accurate hindsight, these may be the only annual spawning event(s).

The overall management objective expands the P-values of water years (up to approximately P = 65%) offering the complete package of access, migration, and spawning for the upper mainstem and all tributaries. Under the proposed real-time release strategy, Bradbury Dam would release 100 cfs on a given day only when that day met all the following criteria: (1) the day occurs within that water year’s adult steelhead migration season with the opening date determined by exceeding the 300 cfs daily average Q threshold at the USGS Lompoc gaging station, and with the closing date always set at April 15, (2) Bradbury Dam is not spilling or releasing outlet flows 137
greater than 100 cfs for flood management, (3) that day is part of a hydrograph’s lost recession limb below San Lucas Bridge (i.e., now captured by Bradbury Dam) that would have followed a Qpk (also captured by Bradbury Dam) exceeding any instantaneous 15 min peak Qpk (the partial flood peak with a 100 cfs baseline) at the USGS Santa Cruz Creek gaging station, and (4) the daily average Q at Santa Cruz Creek on that recession day is 37 cfs or greater (this magnitude explained below).

7.2.2 Proposed Real‐Time Release Strategy
The proposed real-time release strategy requires the following five steps:

Step No.1. Establish the onset of a new adult steelhead migration season. A new migration season begins when the daily average streamflow exceeds 300 cfs at the USGS Lompoc gaging station. The closing date is set at April 15,
Step No. 2. Establish QMinPass threshold for the recommended Bradbury Dam release. A QMinPass of 100 cfs was recommended for preventing the potential bottleneck to adult steelhead migration imposed by the Lompoc Floodplain anticipating some mainstem streamflow loss from a Bradbury Dam release particularly in drier water years (i.e., compliance would be measured at the dam release, not at the USGS Lompoc gage).

Step No. 3. Select a Santa Cruz Creek minimum Qpk partial flood that would trigger the proposed operational protocol (a Qpk less than the minimum would require no action). A Qpk = 100 cfs was recommended as this minimum threshold Qpk for identifying, in real-time, the onset of a significant unimpaired storm event within the migration season specific to the water year.

When the unit runoff of Qpk (100 cfs / 74 mi2
) is weighted by the Bradbury Dam portion of the
drainage area (i.e., 420 mi2 – 219 mi2, with the 219 mi2 being that portion of the entire drainage area above Gibraltar Dam), the targeted Qpk entering Lake Cachuma Reservoir would be approximately 272 cfs (= (100 cfs / 74 mi2) * (420 mi2 - 219 mi2)). 138
Step No. 4. Identify a real-time streamflow threshold for all Santa Cruz Creek storm recession limbs that would trigger an end to the 100 cfs Bradbury Dam release. This entailed two calculations: (a) back-calculating unit runoff at the Santa Cruz Creek gaging station needed to generate an unimpaired 100 cfs at San Lucas Bridge without unimpaired streamflow contribution originating above Gibraltar Dam (100 cfs/(420 mi2 – 219 mi2) = 0.498 cfs/mi2) then (b) multiplying 0.498 cfs/mi2 by 74 mi2 (drainage area at the Santa Cruz Creek USGS gage) which equaled 36.9 cfs, rounded to 37 cfs. A real-time streamflow of 37 cfs on all Santa Cruz Creek storm recession limbs, therefore, would signal termination of the 100 cfs Bradbury Dam release.

When the streamflow at Santa Cruz Creek USGS gage is at 37 cfs, the entire contributing Santa Ynez watershed area excluding the watershed area above Gibraltar Dam (219 mi2 ) would be
producing an approximate unimpaired 100 cfs at San Lucas Bridge.

Step No. 5. As demonstrated for Salsipuedes Creek, LRS days and SSO days are substantial in WYs other than Wet WYs. With the much smaller watershed area downstream of Bradbury Dam, as much of the watershed as possible should be made available to spawning and rearing YOYs. LRS days could be estimated for many spawning destinations. Then successful spawning opportunity days could be modeled following the migration season to evaluate the performance of the proposed protocol. In this manner, real adaptive management could be used to refine the protocol. For example, a 20% shorter duration of days with streamflows equaling or exceeding 100 cfs could be just as effective, provided ‘effective’ is quantifiably defined. Although there are few adult steelhead, any field estimate of migration rate would greatly improve the confidence in modeling SSO days.

This proposed operational protocol for improving annual passage opportunity days offers these advantages: (1) accommodates short duration floods early-season and long duration floods later in the migration season by ending flow releases based on natural recession rates, (2) adjusts for WY type as it unfolds over the season (i.e., can’t predict WY type ahead of time, so avoid method that requires predicting one altogether), (3) mitigates Bradbury Dam effects separately from Gibraltar Dam’s effects (though they can be co-dependent if desired) by weighting the required flow release only by the drainage area controlled by Bradbury Dam and not that of Gibraltar Dam (420 mi2
– 219 mi2), (4) could help open the SYR Lagoon earlier and/or help keep 139
it open longer with 100+ cfs daily streamflows passing the Lompoc Floodplain, and (5) addresses the need for higher passage streamflows below the Narrows and would reduce this migration bottleneck.

7.2.3 Simple Excel Spreadsheet Accounting
Our simple Excel spreadsheet accounting does not model dynamic changes in Lake Cachuma storage or route dam releases downstream. The Fish Passage Supplementation Report for WY2010 (Real-time Decision Group 2010) notes that supplementation releases were predicted to arrive in Solvang (10.5 miles downstream of Bradbury Dam) 12 hours later, but observed 8 hours. ‘H’ Street is approximately 30 miles farther downstream. In the Excel spreadsheet, a 100 cfs dam release experiences no lag (in arrival to a downstream destination) or loss. The primary objective was to justify proposing a different, though not too different, strategy from the Fish Passage Supplementation Program that would provide significantly improved adult migration and spawning. The total annual ac-ft required for these real-time releases can exceed the Fish Passage Supplementation Account, more sophisticated dynamic modeling will be necessary, if this strategy receives further consideration.

7.2.4 Findings
Approximate total annual ac-ft released under the real-time strategy between WY1990 and WY2012 ranged from 0 ac-ft in seven Dry water years and two Extremely Wet water years to an annual maximum total of 13,000 ac-ft in WY1992 (Figure 71). In Dry years, SYR Lagoon did not open using a 300 cfs Qave Lompoc threshold (WY1999, WY2004, WY2012, WY1990, WY2002, WY2009, and WY2007), while in some Extremely Wet years Bradbury Dam spilled early and long (WY1995 and WY1993), with Extremely Wet WY1998 and Wet WY2001 also spilling but requiring releases less than 1000 ac-ft annually. Great variation in total annual ac-ft released was observed among Wet and Above Normal water years. Often this variation was a consequence of timing: when SYR Lagoon opened and when storms arrived. A few example water years are discussed below.
140
Figure 71. Annual total ac-ft real-time Bradbury Dam releases for adult migration and mainstem spawning from WY1990 through WY2012.

Even though WY2009 had a P = 83.9%, a Dry water year, there was an adult migration season that our simple spreadsheet model missed. The 2009 Annual Monitoring Report (REF) notes:
“WY2009 was a dry year (only 13.66 inches of precipitation measured at Bradbury Dam; longterm average is 20.3 inches) with the majority of the rainfall occurring in November, December, and February. On 2/16/09, a storm event caused the sand bar at the mouth of the Santa Ynez River Lagoon to breach. River connectivity to the ocean was maintained after the breach for 30 days ending on 3/17/09. Bradbury Dam did not spill in WY2009.” The instantaneous annual maximum Qpk = 300 cfs for ‘at Narrows nr Lompoc” occurred February 16 on the day of the breach. However our threshold for breaching was Qave > 300 cfs, not Qpk > 300 cfs. USGS Lompoc Qave on February 16 was 89 cfs, with the following day’s Qave = 120 cfs. We had to rely on Qave as our threshold streamflow for breaching because the USGS does not record partial flood peaks for their LSYR gaging stations (i.e., in WY2009 the relatively small annual Qpk WY1990 WY1991 WY1992 WY1993 WY1994 WY1995 WY1996 WY1997 WY1998 WY1999 WY2000 WY2001 WY2002 WY2003 WY2004 WY2005 WY2006 WY2007 WY2008 WY2009 WY2010 WY2011 WY2012 0 2000
4000
6000
8000
10000
12000
14000
0 10 20 30 40 50 60 70 80 90 100
Annual Real‐Time Release (af)
Exceedence Probability (P, %)
141
simply happened to be on February 16 during a Dry water year). The new BiOP should recommend recording partial Qpk’s at Lompoc and ‘H’ Street with a base of 200 cfs or 250 cfs.

Computation of Qave requires waiting the entire day before an average can be computed, but realtime flow management can be practiced with the 15 min flow data online. If our spreadsheet model did establish February 16 the start of the adult migration season, and using the real-time release strategy proposed, Bradbury Dam releases of 100 cfs would have been required 20 days (totaling 4000 ac-ft). Without the releases (i.e., the actual WY2009 hydrographs), Qave > 100 cfs occurred 2 days (spanning the Qpk on February 16) at Lompoc and 1 day at Solvang. Qave’s in Lower Salsipuedes Creek were 67 cfs on February 16, 7.6 cfs on February 17, then 4.3 cfs on February 18. Therefore, adult steelhead migration/spawning would have been restricted to a mainstem event in WY2009.

WY1996, a Blw Norm water year (P = 61.3%), required a total release of 5400 ac-ft (Figure 71).

Lower Salsipuedes Creek streamflows remained mostly below 10 cfs until SYR Lagoon opened (i.e., > 300 cfs at Lompoc) on February 20. In the upper watershed, Santa Cruz Creek experienced two flood peaks: February 20 and March 13. Daily receding streamflows from the substantially bigger first event had just dropped below 37 cfs (on March 11) when the next storm arrived on March 13. Downstream of Bradbury Dam, Solvang streamflows exceeded 100 cfs only 5 days; at Lompoc, 11 days were exceeded. WY1996, therefore, had two modest storm events occurring in the middle of a typical migration/spawning season that were almost perfectly spaced (from a steelhead’s perspective).

WY1994, a Blw Normal water year (P = 54.8%), had two closely spaced, small storm peaks passing Lompoc (February 17 and February 20). Using the guidelines, Bradbury Dam would release 100 cfs for 5 days (February 17 through February 21) totaling 1000 ac-ft. The releases would have improved passage through the Lompoc Floodplain following the February 17 peak (and presumably opening the SYR Lagoon). However, Solvang would have experienced significant improvement for spawning and migration given streamflows did not exceed 100 cfs all year long (maximum Qave = 90 cfs on February 20). By using Santa Cruz Creek, our protocol missed releasing flows for a March 24 to 26 event, because it primarily was a lower watershed event (i.e., no Qpk’s at Santa Cruz Creek to trigger the release). 142

7.2.5 Evaluation Methodology
A quantitative estimate of the benefits derived from a given water year’s dam releases is essential. By way of example, the benefit from releasing 10,400 ac-ft in WY2010 was assessed as follows using passage opportunity days (> 100 cfs at ‘H’ Street) as the quantitative measure for success: (1) the number of passage opportunity days for the WY2010 ‘H’ Street hydrograph with an SYR Lagoon opening date of January 21st (the USGS Lompoc gage exceeded 300 cfs on January 21) was 22 days. However, the 2010 Annual Monitoring Report notes that the sand bar was breached on January 19. This estimate of 22 opportunity days in WY2010 can be located on Figure 16 using P = 23.7%; (2) Using the guidelines for designating which days would require a Bradbury Dam release of 100 cfs, there would be 51 release days: January 20th (SYR Lagoon opening date) through March 13 … when Qave at Santa Cruz Creek dropped below 37 cfs.

Therefore, total passage days in WY2010 went from 22 days to 51 days; (3) Going back to Figure 16, a plot of 51 total annual passage opportunity days at P = 23.7% elevates WY2010 to a good migration year (positioned among the better years in Figure 16), with 22 additional opportunity days above the lower bound line (i.e., 30 opportunity days at P = 23.7%); (4) For perspective, total passage opportunity days under an unimpaired hydrograph in the Pre-Gibraltar Dam Period would have been 104 days, computed by estimating the Qave at Santa Cruz Creek weighted by the entire drainage area above San Lucas Bridge (430 mi2 ) that would produce a 100
cfs Qave passing under San Lucas Bridge (= 17.5 cfs). On the Santa Cruz Creek hydrograph, Qave did not drop below 17.5 cfs until May 3rd (an additional 53 passage opportunity days); (5) A plot of 104 passage opportunity days in Figure 14 (passage opportunity days for Pre-Gibraltar Dam Period) indicates WY2010, if unimpaired, would have exceeded the lower bound line at ‘H’ Street (72 passage days) but was not an uncommonly good migration water year; (6) When comparing contemporary winter streamflows with those during the Pre-Gibraltar Dam Period, our 100 cfs QMinPass at ‘H’ Street is not equivalent (w/r to aiding migration) to the magnitude of pre-Gibraltar daily streamflows typically exceeding 100 cfs.

The 2010 Annual Monitoring Report notes: “There were two passage supplementation releases from Lake Cachuma on 2/6/10 and 4/1/10 that extended steelhead migration potential to over 14 days for each of the two events. Migrating O. mykiss were observed at the mainstem trap during both events. The winter provided passage opportunities for returning southern steelhead 143
particularly during January and the two passage supplementation events. Only one anadromous adult steelhead was observed within the Santa Ynez River basin below Bradbury Dam in WY2010. This fish was captured at the Salsipuedes Creek downstream trap on 3/5/10.” These releases only marginally improved upstream adult migration below Robinson Bridge.

7.2.6 Multiple Purpose Real‐time Bradbury Dam Releases
By releasing 100 cfs from Bradbury Dam on specific non-spill days, daily streamflow accretion downstream will push total mainstem streamflows (accretion + release) higher than 200 cfs on some recession days. WY1996 just discussed was a good example. SYRTAC (2000) and the 2000 BiOp treat any day’s streamflow greater than 25 cfs equally (labeled a passage opportunity day). In our Report we revised minimum passage streamflows and re-examined total annual passage opportunity days accordingly. These minimum passage streamflows were QMinPass = 63 cfs and 88 cfs for Solvang and Lompoc respectively. The Lompoc Floodplain with its broad, rectangular, sandy channelbed generally requires higher streamflows than its QMinPass of 100 cfs (at ‘H’ Street) to encourage adult steelhead migration than required farther upstream. What do we get from a 200 cfs streamflow not provided by a 100 cfs streamflow at ‘H’ Street? Or 100 cfs above Solvang, receiving less flow accretion?

7.2.7 Minimum Passage Streamflows are not Spawning Habitat Streamflows Streamflows providing minimum adult passage do not provide good adult spawning habitat.

High quality spawning habitat requires favorable hydraulic settings (generally the tail-out of pools and runs). A good argument can be made, after observing many spawning steelhead elsewhere, that redd site selection is based primarily on the total hydraulic setting of accelerating flow with contracting depth, rather than choosing ‘preferred’ depths and velocities (and even more suspect, assuming both are chosen independently). In Trush (1991), a simple regression had adults spawning at higher velocities in the bigger streams. Good hydraulics begin at streamflows exceeding section control and approaching active channel control if not slightly greater. Under these streamflows, pool and run tails provide hydraulic settings that encourage spawning over most of the tail-out. Under lesser streamflows, and therefore poorly performing hydraulics, redd selection will be concentrated toward the thalweg. This has at least two undesirable consequences: (1) prospects of redd super-positioning increasing (though not a 144
problem today with so few fish) and (2) redds constructed close to the thalweg are more susceptible to flood scour. Spawning habitat is generally poor below Salsipuedes Creek, and especially so below Robinson Bridge. Therefore, no streamflow range for adult steelhead spawning habitat was investigated. Using our hydraulic control analysis, hydraulically desirable spawning habitat streamflows above Solvang would range from QT Dominant Active Control up to QT Dominant Channel Control, or 124 cfs to 550 cfs (Figure 71). Our QMinPass for Solvang is 63 cfs, below the hydraulic transition point between section and active channel control, and SYRTAC’s QMinPass is 25 cfs still under Dominant Section Control. Therefore, a Bradbury Dam release of 100 cfs improves minimum passage needs, particularly in the Lompoc Floodplain, and generate favorable spawning habitat above Solvang.

7.2.8 Minimum Passage Streamflows are not Migration Streamflows Minimum passage streamflows do not accommodate most adult migration needs. The underlying basis for SYRTAC’s minimum passage analysis was that minimum passage streamflows do not prevent migration, but actually asserting that a minimum passage streamflow does not prevent passage, with no assessment of migration needs attempted. Even if difficult to quantify, it cannot be ignored. This is where the burden-of-proof becomes extremely important when encountering scientific uncertainty.

Minimum passage for the LSYR is an issue of depth and the continuity of minimum depths through shallow riffles (particularly for riffles in broad oblique point bars). It is generally treated as a binary phenomenon (Can they get over the riffle: yes or no?) primarily because there has been no ‘science’ done, other than measuring the depth of an adult steelhead. Justification of an acceptable depth downward, from 0.8 ft all the way down to 0.6 ft (SYRTAC 2000) or lower, is telltale of this narrow ‘passage-only’ perspective. Consideration of a minimum corridor width, to accompany the minimum depth, is an improvement (as discussed regarding the Thompson Method in Report Chapter 4) but again has no science to justify it as migration. Better-than-notpreventing passage is not migration. Migration is behavioral first, rarely is physical limitation first (well, maybe a 20 ft waterfall). Rarely is the streamflow traveling too fast in an alluvial channel such as the Lower Santa Ynez River. The perseverance of adult steelhead to almost climb their way up extremely shallow riffles in small streams is admirable. Adult steelhead react 145
to channel hydraulics and each other. Long runs with shallow, languid streamflow do not encourage rapid migration (i.e., when streamflows are under section control) even though they are easy to swim through. Adult steelhead are stimulated by abrupt changes to streamflow, to shearing flows in pools, and to turbulence. Hydraulically, these flow characteristics begin to commonly appear when rising streamflows begin undergoing active channel control. Long runs and shallow pools have higher velocity cores connecting pool head with pool tail. Deep pools experience shearing flows and deep turbulent eddies. These hydraulic features attract and encourage interaction among fish to migrate.

The same hydraulics favoring spawning habitat creation do favor adult migration but via different hydraulic pathways. Adult steelhead are strongly rheotactic. Long stretches of broad, shallow runs with low velocities at ‘passage streamflows’ present no physical challenge to a swimming adult, but do challenge them behaviorally. As streamflows increase from section control, the LSYR’s string of hydraulic units (i.e., sequence of pools, runs, and riffles) becomes hydraulically connected … as a continuous core of higher velocity streamflow connecting a run’s or pool’s entrance with its tail-out exiting at the downstream RCT. This hydraulic continuity cues a steelhead’s behavioral response to streamflow velocity, and more importantly, to spatial patterns of streamflow velocity.

Steelhead respond to increasing streamflow velocity by spending their time actively swimming upstream more and therefore delaying their migration less. The aim of migration is spawning success. This has been evolutionarily hard-wired into an adult steelhead’s near-fanaticism to keep heading upstream. An adult steelhead is not challenged or fatigued by a uniformly traveling water column at 0.1 ft/sec, 0.5 ft/sec, or even 1.0 ft/sec unless subjected to an experimental treadmill. A river moving at near-0 ft/sec for most its length does not ‘physically allow’ steelhead to swim faster than a river moving at these modestly higher velocities. In fact, if the velocity is very low, steelhead frequently won’t orient themselves upstream. As baseflows increase, and the average or core velocity increases (e.g., on a cross section through the midsection of a long run typical of LSYR), the spatial distribution of all velocities within and among the river’s chain of hydraulic units becomes increasingly complex. The increased hydraulic complexity encourages more rapid upstream migration.
146
Although riffle depth influences migration rate, a steelhead’s behavioral response to streamflow velocity may be the primary determinant for how rapid steelhead move from Point A to Point B, especially when riffles are shallow. Ultimately, this behavioral propensity is expressed biologically but is controlled (at the moment, not evolutionarily) by river hydraulics … and river hydraulics are the by-product of storm events typically associated with other environmental cues, including changing barometric pressure, water temperature, and water clarity.

7.2.9 Refinements/Observations
(1) Our spreadsheet model relied on daily average Santa Cruz Creek streamflows to determine when the threshold 37 cfs was reached, and therefore when the release should stop. Real-time monitoring of the threshold streamflow should be used instead (i.e., when the 15 min streamflow dropped below 37 cfs).
(2) Rapid operational response is always a concern. A Bradbury Dam release, in response to a threshold Qpk in Santa Cruz Creek, would still be effective if it did not begin until the next, or possibly the following day. The day of Qpk and the following day of streamflow recession are typically substantially greater than subsequent recession days. However, rapid response is the best assurance that the more rapid peaking tributaries with their fast recession limbs will still be accessible to migrating adult steelhead. If 10 days, including the day of Qpk, is prescribed then the 10 days would begin with the first day of the release.
(3) Non-spill releases will drop Lake Cachuma Reservoir water level and could delay spilling later into the migration/spawning season than it would otherwise. This possibility was not assessed with our simple spreadsheet.
(4) In drier years, and earlier in the winter as well, a Santa Cruz Creek Qpk can trigger a dam release but then the Santa Cruz Creek streamflow drops below the 37 cfs threshold within 1 or 2 days. A release might not be warranted under these conditions. This might be approached by selecting a higher Santa Cruz Creek Qpk as the release threshold; a higher Qpk would select for a bigger event with a likely longer recession limb. (5) Using the natural recession rate of Santa Cruz Creek storm events will be under-sizing the recession limb’s duration at San Lucas Bridge/Bradbury Dam mainstem channel (though there could be an adjustment factor employed, e.g., make cut-off QSantaCruz for 147
releasing passage streamflows slightly smaller which would extend the flow release period to reflect that of the mainstem channel). In some water years Santa Cruz Creek in March and/or April can have over a month long recession limb with daily average streamflows (e.g., WY1958) all exceeding 35 cfs (i.e., there might need to be a maximum duration above 35 cfs stipulated). However, these large storm events would generally be spilling unless the year before was dry and the reservoir had been drawn down considerably.

7.3 Recommendation No. 3. Real‐time Bradbury Dam Augmentation Releases for Annual Smolt and Juvenile Steelhead Outmigration
Juvenile steelhead in the tributaries below Bradbury Dam have relied on streamflows originating above San Lucas Bridge and SYR’s floodplain groundwater accretion to create favorable rearing and migration conditions in the SYR mainstem. A key management goal is to improve juvenile outmigration by maintaining a continuity of favorable smolt and juvenile steelhead habitats along their entire migration route.

Salsipuedes Creek is one of the largest tributaries below Bradbury Dam with good juvenile rearing habitat and persistent summer streamflows. It can serve as a litmus test for future management. Improving minimum connectivity by managing for a greater positive differential in days (Table 3 and Figure 52) is still managing for the minimum. Migrating smolts and juveniles from Salsipuedes Creek require more than minimal mainstem conditions to survive and grow.

For more productive downstream passage conditions, rather than baseflows on the threshold of disconnectivity, juveniles and smolts leaving Salsipuedes Creek need to encounter mainstem passage streamflows or (better) migration streamflows. QJuvMinPass is the minimum passage streamflow threshold for smolts/juvenile steelhead associated with Section Hydraulic Control on the RCT-Q rating curves. For Salsipuedes Creek, QJuvMinPass equals 4.0 cfs (Figure 72); for SYR ‘H’ Street, QJuvMinPass = 7.0 cfs (Figure 56A). QJuvMinMigr is the minimum migration streamflow threshold for smolts/juvenile steelhead associated with Dominant Section Hydraulic Control on the RCT-Q rating curve. For Salsipuedes Creek, QJuvMinMigr equals 22 cfs; For SYR ‘H’ Street, QJuvMinMigr equals 38 cfs.

Figure 72
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Table 7. Last day in recession hydrograph when the daily average streamflow was greater than, or equal to, the minimum juvenile passage streamflow for Salsipuedes Creek (QJuvMinPass = 4.0 cfs)(Figure 72) and Santa Ynez River at ‘H’ Street nr Lompoc (QJuvMinPass = 7.0 cfs)(Figure 56A).

WY
Last Day QJuvMinPass
Lower Salsipuedes
Creek (4.0 cfs)
Last Day QJuvMinPass
Santa Ynez River at
‘H’ Street (7.0 cfs)
Difference
(days)
WY2000 June 22 June 3 -19
WY2001 June 21 June 7 -14
WY2002 <March 01 March 11 +10
WY2003 <March 01 May 16 +77
WY2004 March 4 <March 01 -3
WY2005 July 10 July 09 -1
WY2006 June 2 June 20 +18
WY2007 <March 01 March 03 +2
WY2008 April 11 April 17 +6
WY2009 <March 01 March 07 +6
WY2010 March 30 May 04 +35
WY2011 June 19 July 03 -14
WY2012 <March 01 <March 01 NA
WY2013 <March 01 <March 01 NA
To improve the annual outcomes in Table 7, four key hydrological/hydraulic relationships were used to quantify the magnitude, duration, frequency, and timing of real-time Bradbury Dam releases: (1) the RCT-Q ‘H’ Street rating curve was used to identify streamflow thresholds for the lower SYR mainstem Section and Dominant Section controls (Figure 56A), (2) the RCT-Q rating curve for Salsipuedes Creek to identify the same two hydraulic thresholds for Section and 150
Dominant Section controls (Figure 72), (3) annual Salsipuedes Creek hydrographs to establish when smolts/juveniles could be entering the SYR mainstem, and (4) annual hydrographs for Santa Cruz Creek to estimate unimpaired streamflows at ‘H’ Street for the purpose of recommending the magnitude and timing of real-time Bradbury Dam augmentation releases. The basic framework for applying these four relationships is as follows:

Step No. 1. The smolt and juvenile steelhead outmigration season would begin:

Early Outmigration Season: Starting on the first day of a new calendar-year (i.e., January 1), the date when Salsipuedes Creek streamflow first exceeds 4.0 cfs (therefore exceeding Section Hydraulic Control on the Salsipuedes Creek RCT-Q curve (Figure 72), and promoting juvenile passage) would initiate Bradbury Dam augmentation releases.

Late Outmigration Season: If Salsipuedes Creek streamflows never exceed 4.0 cfs by February’s end, then beginning the first day in March, the date when Salsipuedes Creek streamflow first exceeds 1.0 cfs (therefore becomes re-connected to the mainstem) would initiate Bradbury Dam augmentation releases.

Step No. 2. During Early-Season or Late-Season outmigration seasons, Bradbury Dam augmentation releases would be made using these two streamflow thresholds:

If Santa Cruz Creek streamflow >= 6.5 cfs, then the Bradbury Dam augmentation release would provide 38 cfs at ‘H’ Street (for downstream smolt/juvenile steelhead migration).

If Santa Cruz Creek streamflow < 6.5 cfs and >= 1.2 cfs, then the Bradbury Dam augmentation release would provide 7.0 cfs at ‘H’ Street (for downstream smolt/juvenile steelhead passage).

When the gaged streamflow at Santa Cruz Creek = 6.5 cfs, the estimated unimpaired streamflow at San Lucas Bridge equals: 6.5 cfs * 5.8 = 37.7 cfs, rounded to 38.0 cfs (where: 430 mi2 / 74 mi2 = 5.81, or the ratio of the DA at San Lucas Bridge / DA at the USGS Santa Cruz Creek gage). In words: whenever Santa Cruz Creek was flowing at 6.5 cfs or greater, the unimpaired streamflow at ‘H’ Street was at least 38 cfs, the threshold streamflow corresponding to Dominant Section Hydraulic Control on the ‘H’ Street RCT-Q rating curve (Figure 65A). 151
When the gaged streamflow at Santa Cruz Creek equals 1.2 cfs, the estimated unimpaired streamflow at San Lucas Bridge equals: 1.2 cfs * 5.8 = 6.96 cfs, rounded to 7.0 cfs. In words:
whenever Santa Cruz Creek was flowing at 1.2 cfs or greater, the unimpaired streamflow at ‘H’ Street was at least 7.0 cfs, the threshold streamflow corresponding to Section Hydraulic Control on the ‘H’ Street RCT-Q rating curve (Figure 65A).

Step No. 3. When gaged Santa Cruz Creek streamflow drops < 1.2 cfs, then Bradbury Dam augmentation releases cease. Note that this provision could still allow ‘H’ Street streamflow to drop below its disconnectivity threshold of 2.7 cfs even though juveniles could still be entering the mainstem from Salsipuedes Creek.

Step No. 4. Compliance would be measured at USGS Gaging Station No.11134000 Santa Ynez River at ‘H’ Street nr Lompoc (allowing for downstream flow lag) to ensure minimum passage and minimum migration streamflows are being met when smolts/juveniles would be leaving Salsipuedes Creek (and presumably other tributaries as well, including Hilton Creek).

The sharp drop in mainstem streamflows between the USGS Gage above Robinson Bridge and the ‘H’ Street gaging station downstream will make compliance difficult. This ‘H’ Street juvenile migration bottleneck was highlighted by the WY2014 winter hydrograph.

WY2014 has had a total annual precipitation at Gibraltar Dam of 11.24 inches as of April 28, 2014, following WY2013 which had the least total annual precipitation (8.50 inches) on record.

Although a very poor pair of water years for steelhead, Salsipuedes Creek did experience one rainfall event in late-February to early-March 2014 (Figure 73). This storm’s timing and magnitude was encouraging for two cohorts of juvenile steelhead to out-migrate. If juveniles had survived in Lower Salsipuedes Creek, they would likely have taken advantage of this storm.

However, their survival in the SYR mainstem would have been questionable.

Provisional streamflow data collected at the SYR mainstem USGS gaging station below Salsipuedes Creek but upstream of Robinson Bridge (Figure 74) documents the arrival and passage of the Salsipuedes Creek storm flows (with only minor additional contributions from upstream). Salsipuedes juveniles would experience a connected mainstem channel down to this USGS gage but with poor productivity (biological productivity requires weeks of inundation to develop) and growth potential. Farther downstream however, the provisional USGS streamflow data coll
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References
Alagona, P. S., S. D. Cooper, M. Capelli, and P. H. Beedle. (2012). A History of Steelhead and Rainbow Trout (Oncorhynchus mykiss) in the Santa Ynez River Watershed, Santa Barbara County, California. Southern Acad. Sci. 111(3): 163-222.

Armantrout, N.B., Compiler. (1998). Glossary of Aquatic Habitat Inventory Terminology.

American Fisheries Society, Bethesda, Maryland.

Barnhart, R.A. (1986). Species profiles: life histories and environmental requirements of coastal fishes and invertebrates (Pacific Southwest)- Steelhead. U.S. Fish Wild. Serv. Biol. Rep. 82(11.60). U.S. Army Corps of Engineers, TR EL-82-4. 21 pp.

Braca, G. (2008). Stage–discharge relationships in open channels: Practices and problems.

FORALPS Technical Report, 11. Università degli Studi di Trento, Dipartimento di Ingegneria Civile e Ambientale, Trento, Italy, 24 pp.

Cachuma Operation and Maintenance Board. (2008). Annual monitoring report and trend analysis for 2005–2008 for the biological opinion for the operation and maintenance of the Cachuma Project on the Santa Ynez River in Santa Barbara County, California. Prepared for the National Marine Fisheries Service, Southwest Region, and U.S. Department of Reclamation, South Central California Area Office, by the Cachuma Operation and Maintenance Board, Santa Barbara, CA.126 pp. + Appendices.

Cachuma Operation and Maintenance Board. (2012). 2009 Annual Monitoring Report and Trend Analysis for The Biological Opinion for the Operation and Maintenance of the Cachuma Project on the Santa Ynez River in Santa Barbara County, California. Prepared for: U.S. Department of the Interior, Bureau of Reclamation, South Central California Area Office. 112 pp. + Appendices.
157
(CDFG) California Department of Fish & Game. (2012). Standard operating procedure for critical riffle analysis for fish passage in California. DFG-IFP-001, CDFG Instream Flow Program, 26.

Denton, D. (1989). Draft Santa Ynez Instream Flow Need Study. Northern District. CA Department Water Resources. 59 pp.

Evenson, R. E. (1966). Hydrologic Inventory of the Lompoc Subarea, Santa Ynez River Basin, Santa Barbara County, California 1957-62. USGS Water Resources Division, Open-File Report 66-42.

Fukushima, L. and E. W. Lesh. (1998). Adult and juvenile anadromous salmonid migration timing in California streams. California Fish and Game 84: 133-145.

Hayes, S. A., M. H. Bond. C. V. Hanson, E. V. Freund, J. J. Smith, E. C. Anderson, A. J.

Ammann, and R. B. MacFarlane. (2008). Steelhead growth in a small central California watershed: upstream and estuarine rearing patterns. Transactions of the American Fisheries Society 137(1):114-128.

Kelley, E. (2008). Steelhead Smolt Survival in the Santa Clara and Santa Ynez River Estuaries.

Prepared for The California Department of Fish and Game. University of California, Santa Barbara, p. 61.

McBain and Trush and Trout Unlimited. (2000). Allocating Streamflows to Protect and Recover Threatened Salmon and Steelhead Populations in the Russian River and other Northcoast Rivers in California. Commentary No.3 to the State Water Resources Control Board. July 27, 2000. 38 pp. + Appendices.

McBain and Trush. (2012). Evaluating Priority Life History Tactics for Re-Introduced Alameda Creek Steelhead. Prepared for: Alameda Creek Fisheries Restoration WorkGroup, 112 pp.
158
Montgomery, D.R. and L. H. MacDonald. (2002). Diagnostic approach to stream channel assessment and monitoring. Journal of the American Water Resources Association 38(1):1-16.

Moore, M.R. (1980). Factors influencing the survival of juvenile steelhead rainbow trout (Salmo gairdneri gairdneri) in the Ventura River, California. MS Thesis, Humboldt State University, June 1980, 82 pp.
(NMFS) National Marine Fisheries Service. (2000). Endangered species act section 7 consultation. Biological opinion. U.S. Bureau of Reclamation operation and maintenance of the Cachuma Project on the Santa Ynez River in Santa Barbara County, California. National Marine Fisheries Service, Southwest Region. 276 pp.

Real-time Decision Group. (2010). Report on the 2010 fish passage supplementation program.

Real-time decision group and Cachuma project biology staff. For: Adaptive Management Committee. November 30, 2010. 19 pp.
(SYRTAC) Santa Ynez River Technical Advisory Committee. (1997). Proposed Investigations to Determine Fish-Habitat Management Alternatives for the Lower Santa Ynez River, Santa Barbara County: 1997 Update. June 1997.
(SYRTAC) Santa Ynez River Technical Advisory Committee. (1999). Habitat Analysis. Project No. 380802. February 5, 1999. SWRCB Exhibit CT-36.
(SYRTAC) Santa Ynez River Technical Advisory Committee. (1999). Adult steelhead passage analysis for the Santa Ynez River. Draft report. Prepared for Santa Ynez River Consensus Committee.
(SYRTAC) Santa Ynez River Technical Advisory Committee. (2000). Appendix B. Flow-related fish enhancement in the Santa Ynez River. Prepared for: Santa Ynez River Consensus Committee. Prepared by: Conjunctive Use Work Group. October 2, 2000. pp. B-4-3 & B4-4. 159
(SYRTAC) Santa Ynez River Technical Advisory Committee. (2009). Summary and analysis of annual fishery monitoring in the Lower Santa Ynez River: 1993-2004. Prepared by:

SYRTAC Adaptive Management Committee. June 30, 2009.

Shapovalov, L. (1944). Preliminary report on the fisheries of the Santa Ynez River system, Santa Barbara County, California. CDFG, Branch Administrative Report No. 44-14, submitted September 13, 1944. 22 pp.

Statzner, B. (1988). Hydraulic stream ecology – Observed patterns and potential applications.

Journal of the North American Benthological Society 7(4):307-360.

Titus, R. G., D. C. Erman, and W. M. Snider. 2006. History and status of steelhead in California coastal drainages south of San Francisco Bay. In draft. California Dept of Fish and Game.

Fish Bulletin. 293 p.

Trush, W. 1991. The Influence of channel morphology on spawning steelhead trout in South Fork Eel River tributaries. PhD Dissertation, Department of Forestry and Natural Resource Management, University of California, Berkeley, CA.

Thompson, K. (1972). Determining stream flows for fish life. p. 31-50 in: Proc Intream Flow Requirement Workshop. Pacific Northwest River Basins Commission. Portland, Oregon.

Thompson, G. G. (1991). Determining Minimum Viable Populations under the Endangered Species Act, NOAA Tech. Memo. NMFS F/NWC-198. 78 pp.

U.S. Bureau of Reclamation. (2011). 2008 Annual monitoring report and trend analysis for 2005-2008 for the biological opinion for the operation and maintenance of the Cachuma project on the Santa Ynez River in Santa Barbara County, California. Prepared for:

National Marine Fisheries Service. 126 pp. + Appendices.

U.S. Bureau of Reclamation. (2013). 2010 Annual monitoring report and trend analysis for 2005-2008 for the biological opinion for the operation and maintenance of the Cachuma 160
Project on the Santa Ynez River in Santa Barbara County, California. Prepared for:

National Marine Fisheries Service. 135 pp. + Appendices.

Ward, J. (1989). The 4-dimensional nature of lotic ecosystems. Journal of the North American Benthological Society 8(1):2-8.

SOUTH-CENTRAL/SOUTHERN CALIFORNIA COAST STEELHEAD

RECOVERY PLANNING DOMAIN
5-Year Review:

Summary and Evaluation of
South-Central California Coast Steelhead Distinct Population Segment San Carpoforo Creek Steelhead (Mark H. Capelli)
National Marine Fisheries Service
West Coast Region
California Coastal Office, Santa Rosa, California
2016

Note: This document should be cited as:

National Marine Fisheries Service. 2016. 5-Year Review: Summary and Evaluation of SouthCentral California Coast Steelhead Distinct Population Segment. National Marine Fisheries Service. West Coast Region. California Coastal Office. Santa Rosa, California.

5-YEAR REVIEW
South-Central/Southern California Coast Steelhead Recovery Planning Domain: South-Central California Coast Steelhead DPS
Species Reviewed Evolutionarily Significant Unit or
Distinct Population Segment
Steelhead (Oncorhynchus mykiss) South-Central California Coast Steelhead DPS

1.0 GENERAL INFORMATION

1.1 Preparers and Reviewers

1.1.1. West Coast Region
Preparer:

Mark H. Capelli, South-Central/Southern California Coast Steelhead Recovery Planning Coordinator, 113 Harbor Way, Suite 150, Santa Barbara, California 93101 (805) 963-6478
Reviewer:

Joyce Ambrosius, West Coast Region, NOAA Fisheries, 777 Sonoma Avenue, Room 325, Santa Rosa, California 95404-6515 (707) 575-6064

1.1.2. Southwest Fisheries Science Center, Santa Cruz Laboratory Dr. David Boughton, Chair, South-Central/Southern California Steelhead Technical Recovery Team, 110 Shaffer Road, Santa Cruz, California 94920-1211 (831) 420-3920

1.2 Introduction
The South-Central California Coast Distinct Population Segment (DPS) is listed as threatened and is comprised of a suite of steelhead populations (Oncorhynchus mykiss) that inhabit coastal stream networks from the Pajaro River south to, but not including the Santa Maria River.

Freshwater-resident (non-anadromous) O. mykiss, commonly known as rainbow trout, also occur in the same geographic region, frequently co-occurring in the same river systems as the anadromous form. Clemento et al. (2009) found that O. mykiss above and below impassable dams within the South-Central Coast DPS tended to be each other’s closest relatives, suggesting that each steelhead DPS is simply the anadromous component of a corresponding Evolutionarily Significant Unit (ESU; Waples 1991) comprising both anadromous and resident O. mykiss.

Anadromous and/or freshwater forms of the species also occur in some basins south of the U.S. border, on the Baja California Peninsula (Ruiz-Capos and Pister 1995). 1 West Coast salmon and steelhead (Oncorhynchus spp.) stocks have declined substantially from their historic numbers and many now are threatened with extinction. Multiple factors have contributed to the declines of individual populations. These include the loss of freshwater and estuarine habitat, periodic poor ocean conditions, and a variety of land-use, flood control and water management practices which have impacted many watershed-wide processes; these include sedimentation and hydrologic processes which create and sustain essential steelhead habitats. These factors collectively led to the National Marine Fisheries Service (NMFS) to list south-central California coast steelhead (the anadromous form of O. mykiss) as threatened under the ESA in 1997 (Figure 1).

Section 4(c)(2) of the ESA directs the Secretary of Commerce to review the listing classification of threatened and endangered species at least once every five years. After completing this review, the Secretary must determine if any species should be: (1) removed from the list; (2) have its status changed from threatened to endangered; or (3) have its status changed from endangered to threatened. The most recent listing determinations for salmon and steelhead occurred in 2005 and 2006. This document reflects the agency’s 5-year review of the ESA-listed South-Central California Coast Steelhead Distinct Population Segment (SCCCS DPS) since the last status review in 2010 (Williams et al. 2011).
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Figure 1. South-Central California Coast Steelhead DPS. 3 1.3 Methodology used to complete the review
Section 4(c) (2) of the ESA requires 5-year status reviews for all listed species to determine if a change in status is necessary. A public notice initiating this review and requesting information was published on February 6, 2015, with a 90-day response period (80 FR 6695).

This 5-year status review was conducted by NOAA Fisheries Regional Staff and Southwest and Northwest Fisheries Science Center and West Coast Regional personnel. The review relied principally on 2016 viability assessment update prepared by NOAA’s Fisheries Science Centers, Technical Memoranda prepared by NOAA Southwest Fisheries Science Center, Santa Cruz Laboratory, DPS wide threats assessments prepared for the South-Central California Steelhead Recovery Plan, and run-size data from a small number of watersheds where such data is regularly collected.

NOAA’s Southwest and Northwest Science Centers reviewed all new and substantial scientific information since the most recent review in 2010 and produced an updated viability summary report for the listed salmon and steelhead in California. The purpose of their review is to determine whether or not the biological status of the South-Central California Coast Steelhead DPS had changed since the 2010 status review. NOAA staff from California Coastal Office, Santa Rosa reviewed the status report and assessed whether the five ESA listing factors (threats) had changed substantially since the most recent listing 2006 determination (71 FR 5248).

1.4 Background – summary of previous reviews, statutory and regulatory actions, and recovery planning

1.4.1 FR Notice citation announcing initiation of this review 80 FR 6695 February 6, 2015

1.4.2 Listing history
Table 1. Summary of the listing history under the Endangered Species Act for the SouthCentral California Coast Steelhead DPS.

Salmonid Species ESU/DPS Name Original Listing Revised Listing Steelhead
Anadromous
O. mykiss
South-Central California
Coast Steelhead DPS
FR Notice: 62 FR 43937
Date Listed: 08/18/1997
Classification: Threatened
FR Notice: 71 FR 5248
Date: 01/05/2006
Reconfirmed Classification:

Threatened
4 1.4.3 Associated rulemakings
Table 2. Summary of rulemaking for 4(d) protective regulations and critical habitat for the South-Central California Coast Steelhead DPS.

Salmonid Species ESU/DPS Name 4(d) Protective
Regulations
Critical Habitat
Designations
Steelhead
Anadromous
O. mykiss
South-Central California
Coast Steelhead DPS
FR Notice: 70 FR 37160
Date: 06/28/2005
FR Notice: 70 FR 52488
Date: 09/02/2005

1.4.4 Review History
The first comprehensive status review of steelhead was conducted by Busby et al. (1996), who characterized Evolutionarily Significant Units (ESUs) using the conceptual framework of Waples (1991), and then assessed extinction risk of each ESU. The South-Central California Coast Steelhead ESU was subsequently listed as threatened by NMFS under the US Endangered Species Act in l997. The listing was modified (2006) to include only the anadromous component of the ESU, which is composed of both anadromous and freshwater-resident forms of O. mykiss.

Good et al. (2005) updated the status of Pacific coast steelhead populations, and another update was conducted in 2010 (Williams et al. 2011). None of these updates led to changes in the status of the listed DPS, which has remained threatened.

Consistent with the requirements of the ESA, the listing triggered the preparation of a recovery plan for the South-Central California Coast Steelhead DPS. The first phase of recovery planning focused on the synthesis of scientific information and developing technical guidance for recovering the DPS, and was conducted by NOAA Southwest Fisheries Science Center, Santa Cruz Laboratory and its scientific partners. This phase of planning was based on available scientific information and a conceptual framework for viable salmonid populations (McElhany et al. 2000). Findings are described in a series of NMFS Technical Memoranda describing ESU structure (Boughton et al. 2006, Boughton and Goslin 2006), viability criteria (Boughton et al. 2007), research needs (Boughton 2010c), a conceptual framework for recovery (Boughton 2010a), and a conceptual plan for ongoing monitoring the risk status of California costal salmonid populations (Adams et al. 2011).

The second phase focused on preparation of a recovery plan that identified threats, recovery actions, research, monitoring and adaptive management issues, and described strategies and goals for recovering, and ultimately de-listing, the DPS. Since the last status review update (2010), NMFS has completed and formally adopted a recovery plan for the South-Central California Coast Steelhead DPS (National Marine Fisheries Service 2013). The recovery plan is based on the biological needs of the fish and provides a foundation for restoring the DPS and its constituent populations to levels at which they would no longer be considered at risk of extinction.

These “levels” of risk are formally known as viability criteria, and the summary statistics used to assess the DPS are known as viability metrics (Figure 2). With the publication of the South5

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Central California Steelhead Recovery Plan and a conceptual monitoring plan, the goal of statusreview updates now becomes an assessment of whether viability metrics for the DPS are moving toward or away from the viability criteria. Unfortunately, this simple process of reviewing the status of the DPS is currently hampered by two problems: 1) scientific uncertainty about the viability criteria themselves, and 2) incomplete data on viability metrics. To address #1, below we review new information relevant to the viability criteria. To address #2, we review the implementation thus far of the monitoring plan, known formally as the California Coastal Monitoring Plan (CMP). See Sections 2.1.4 and 2.3 below.

Figure 2. Concept of viability metric and a viability criterion applied to a hypothetical population.

Table 3. Summary of previous scientific assessments for the South-Central California Coast Steelhead DPS.

Salmonid Species ESU/DPS Name Document Citation
Steelhead
Anadromous O. mykiss
South-Central California
Coast Steelhead DPS
Williams, T. H. et al. 2011. Status Review Update for
Pacific Salmon and Steelhead Listed Under the Endangered Species Act. NOAA’s Southwest Fisheries Science Center.

Boughton, D. A. 2010c. Some Research Questions on
Recovery of Steelhead on the South-Central and Southern California Coast. NOAA-TM-NMFS-SWFSC-467.

Clemento, A. J. et al. 2009. Population Genetic Structure and Ancestry of Oncorhynchus mykiss Populations Above
6 and Below Dams in South-Central California. Conservation Genetics 10:1321-1336.

Pearse, D. and J. C. Garza. 2008. Historical Baseline for Genetic Monitoring of Coastal California Steelhead,
Oncorhynchus mykiss. Final Report for California
Department of Fish and Wildlife Fisheries Restoration
Grant Program P0510530.

Garza, J. C. and A. Clemento. 2007. Population Genetic
Structure of Oncorhynchus mykiss in the Santa Ynez River, California. Final Report for Project Partially Funded by the Cachuma Conservation Release Board.

Boughton, D. A. et al. 2007. Viability Criteria for Steelhead of the South-Central and Southern California Coast.

NOAA-TM-NMFS-SWFSC-407.

Jackson, T.A. 2007. California Steelhead Fishing ReportRestoration Card: A Report to the Legislature. California Department of Fish and Wildlife, Sacramento, California.

Girman, D. and J. C. Garza. 2006. Population Structure
and Ancestry of O. mykiss populations in South-Central
California Based on Genetic Analysis of Microsatellite
Data. Final Report for California Department of Fish and Wildlife Project No. P0350021 and Pacific State Marine
Fisheries Contract No. AWIP-S-1.

Boughton, D. A. et al. 2006. Steelhead of the SouthCentral/Southern California Coast: Population Characterization for Recovery Planning NOAA-TMNMFS-SWFSC-394.

Boughton, D. A. and M. Goslin. 2006. Potential Steelhead Over-Summering Habitat in the South-Central/Southern
California Coast Recovery Domain: Maps Based on the
Envelope Method NOAA-TM-NMFS-SWFSC-391.

Boughton, D. A et al. 2005. Contraction of the Southern Range Limit for Anadromous Oncorhynchus mykiss.

NOAA-TM-NMFS-SWFSC-380.

Helmbrecht, S and D. A. Boughton. 2005. Recent Efforts to Monitor Anadromous Oncorhynchus Species in the
California Coastal Region: A Complication of Metadata
NOAA-TM-NMFS-SWFSC-381.

Good, T. P. et al. (eds.) 2005. Updated Status of Federally Listed EUS of West Coast Salmon and Steelhead. NOAATM-NWFSC-66. 7 I I I

1.4.5 Species’ Recovery Priority Number at start of 5-year review NOAA Fisheries issued guidelines in 1990 (55 FR 24296) for assigning listing and recovery priorities. Three criteria are assessed to determine a species’ priority for recovery plan development, implementation, and resource allocation: 1) magnitude of threat; 2) recovery potential; and 3) existing conflict with activities such as construction and development. The recovery priority number for the subject DPS, as reported in the 2008-20010 Biennial Report to Congress on the Recovery Program for Threatened and Endangered Species (available at: http://www.nmfs.noaa.gov/pr/pdfs/laws/esabiennial2008.pdf) is listed in Table 4 below.

1.4.6 Recovery Plan or Outline
Table 4. Recovery Priority Number and Endangered Species Act Recovery Plans for the South-Central California Coast Steelhead DPS.

Salmonid Species ESU/DPS Name
Recovery
Priority
Number
Recovery Plans/Outline
Steelhead
Anadromous O. mykiss
South-Central California
Coast Steelhead DPS 3
Final Recovery Outline - 2007
Draft Recovery Plan - 2009
Final Recovery Plan - 2013
The recovery priority number “3” for the South-Central California Coast Steelhead DPS is based on a high magnitude of threat to a small number of extant populations vulnerable to extirpation due to loss of accessibility to freshwater spawning and rearing habitat, low abundance, degraded estuarine habitats, and altered watershed processes essential to maintain freshwater habitats. The recovery potential is low to moderate due to the lack of additional populations, lack of available/suitable freshwater habitat, fish passage barriers, and inadequate instream flow. There is a moderate magnitude of threat to smaller watersheds, and higher risk in larger watersheds with major water supply and flood control facilities. Conflict was determined to be present due to existing and anticipated future development, habitat degradation, and conflict with land development and associated flood control activities and water supplies.

2.0 REVIEW ANALYSIS

2.1 Delineation of Species under the Endangered Species Act

2.1.1 Is the species under review a vertebrate?
ESU/DPS Name YES NO
South-Central California Coast Steelhead
DPS
X
8 I I I
I I I

2.1.2 Is the species under review listed as a DPS?
ESU/DPS Name YES NO
South-Central California Coast Steelhead
DPS
X

2.1.3 Was the DPS listed prior to 1996?
ESU/DPS Name YES NO Date Listed if
Prior to 1996
South-Central California Coast Steelhead
DPS
X n/a

2.1.3.1 Prior to this 5-year review, was the DPS classification reviewed to ensure it meets the 1996 policy standards?
In 1991 NMFS issued a policy to provide guidance for defining ESUs of salmon and steelhead that would be considered for listing under the ESA (56 FR 58612; November 20, 1991). Under this policy a group of Pacific salmon populations is considered an ESU if it is substantially reproductively isolated from other con-specific populations and it represents an important component in the evolutionary legacy of the biological species. This DPS was originally defined and listed under NMFS’s ESU policy in 1997. The 1996 joint NMFS-U.S. Fish and Wildlife Service (FWS) DPS policy affirmed that a stock of Pacific salmon (or steelhead) was considered a DPS if it represented an ESU of a biological species and concluded that NMFS’ ESU policy was a detailed extension of the joint DPS policy. Accordingly, NMFS considered the originally defined and listed ESU to be a distinct population segment under the ESA. After reassessing the status of steelhead ESUs in 2005, NMFS decided to use the joint NMFS-FWS DPS policy to define steelhead only DPSs and in 2006 announced final listing determinations for steelhead based on the DPS policy (71 FR 834). That analysis concluded that South-Central California Coast Steelhead constituted a DPS under the joint DPS policy and that it continued to be a threatened species. In summary, therefore, the South-Central California Coast Steelhead DPS has been found to meet the 1996 DPS policy standards.

2.1.4 Summary of relevant new information regarding the delineation of the ESUs/DPSs under review
Since publication of the last status review (Williams et al. 2011), significant new genetic data are available for steelhead populations across much of coastal California.

Recent work indicates that the tendency to out-migrate (versus maturing in freshwater) is associated with particular juvenile body sizes, gender, the presence of a particular “supergene” on chromosome Omy5, and interactions of these effects. Both variants of the supergene occur in most populations, but one variant tends to predominate in sites with connectivity to the ocean, and the other in populations without connectivity. Overall, these results show that the resident and anadromous forms are tightly integrated at the population level, suggesting a revision of the viability criterion for 100% anadromous fraction. However, such revision would require 9 I I I
I I I
I I I
additional quantitative analysis of population viability. See further discussion in Section 2.3 below.

2.2 Recovery Criteria

2.2.1 Do the species have final, approved recovery plans containing objective, measurable criteria?
ESU/DPS Name YES NO
South-Central California Coast Steelhead
DPS
X
A recovery plan has been prepared for the South-Central California Coast Steelhead DPS (National Marine Fisheries Service 2013). The recovery plan contains objective measurable recovery criteria for both individual populations and the DPS as a whole based upon the viability criteria developed by NOAA Southwest Fisheries Science Center, Santa Cruz Laboratory and the recovery strategy developed by NOAA Fisheries, California Coastal Offices, Santa Rosa and Long Beach (Boughton et al. 2007). These criteria specify a minimum number of populations distributed through four distinctive biogeographic population groups within the DPS which must exhibit a suite of biological characteristics, including minimum annual run-size, life-history diversity, persistence through long-term oceanic conditions, population and spawning density, and an anadromous fraction.

2.2.2 Adequacy of recovery criteria

2.2.2.1 Do the recovery criteria reflect the best available and most up-to date information on the biology of the species and its habitat? ESU/DPS Name YES NO
South-Central California Coast Steelhead
DPS
X
The provisional recovery criteria reflect the best available and most up to date information on the biology of the species, based upon the viability criteria developed NOAA Southwest Fisheries’ Science Center, Santa Cruz Laboratory. The South-Central California Steelhead Recovery Plan has undergone independent scientific peer and co-manager review.

2.2.2.2 Are all of the 5 listing factors that are relevant to the species addressed in the recovery criteria?
ESU/DPS Name YES NO
South-Central California Coast Steelhead
DPS
X
10 2.2.3 List the recovery criteria as they appear in any final or interim recovery plan, and discuss how each criterion has or has not been met, citing information
The South-Central California Coast Steelhead Recovery Plan contains objective measurable recovery criteria based upon the viability criteria developed by NOAA’s Southwest Fisheries Science Center and the recovery strategy developed by NOAA Fisheries’ West Coast Region, California Coastal Offices, Long Beach and Santa Rosa.

Population-Level Criteria
Mean Annual Run-Size - Each population identified as a core population within each of the 4 Biogeographic Population Groups (BPG) must meet the mean annual run-size. In some cases the population may be comprised of two or more closely interacting watersheds. This numeric criterion is subject to modification pending further research, and may differ for individual populations. See Figure 3, Tables 5 and 6.

Ocean Conditions - Each population identified as a core population within each of the 4 BPGs must meet the mean annual run-size during variable oceanic conditions over the course of at least 6 decades. In some cases the population may be comprised of two or more populations from closely interacting watersheds. This criterion will require multi-decadal monitoring; currently the monitoring of individual populations is inadequate to assess how they meet this criterion. See section 4.0 Recommendations for Future Actions below.

Population Density - Each population identified as a core population within each of the 4 BPGs must meet the density criteria (currently unspecified pending further research). In some cases the population may be comprised of two or more closely interacting watersheds. Further research is needed on this criterion; currently the monitoring of individual populations is inadequate to assess how they meet this criterion. See section 4.0 Recommendations for Future Actions below.

Anadromous Fraction - The portion of each of the populations identified as a core population within each of the 4 BPGs that is counted towards the meeting the population size criteria must be comprised of 100% anadromous individuals. In some cases the population may be comprised of two or more closely interacting watersheds. This numeric criterion is subject to modification pending further research. See Section 4.0 Recommendations for Future Actions below. 11 r '
i
'1
I
)
/
,,
/ ~
/
/
-7
~ · ~ -1.

L---7
l
Figure 3. Four Biogeographic Population Groups (BPGs) making up the South-Central California Coast Steelhead DPS.
12 DPS-Level Criteria
Biogeographic Diversity - A minimum number of viable populations must be distributed through each of the 4 BPGs. These viable populations must inhabit watersheds with drought refugia and be separated a minimum of 68 km to the maximum extent possible. The recovery plan identifies a minimum suite of core populations within each BPG, including those portions of the watersheds that contain drought refugia. See Tables 5 and 6. Further research is needed on this criterion, in particular the identification of drought refugia in the core watersheds. See Section

4.0 Recommendations for Future Actions below.

Life-History Diversity - The viable populations within each BPG must exhibit the three principal steelhead life-history types (fluvial-anadromous, lagoon-anadromous, and freshwater resident).

The recovery plan identifies a suite of core populations in each biogeographic population group with habitats having the intrinsic potential to support the three principal life-history types. New findings demonstrate that resident and anadromous life-histories in O. mykiss in the SouthCentral California Coast Steelhead Recovery Planning Area are tightly integrated. This in turn suggests that the viability criterion for a 100% anadromous fraction in core populations (Table 6) should be revised. However, the studies summarized below do not include any populationviability analyses, which would be necessary for proposing a specific revision of the criterion.

2.3 Updated Information and Current Species Status

2.3.1 Analysis of Viable Salmonid Population (VSP) Criteria There is little new evidence to suggest that the status of the South-Central California Coast Steelhead DPS has changed appreciably in either direction since publication of the last status review (Williams et al. 2011). New and additional information available on anadromous runs since Williams et al. (2011) remains limited and does not appear to suggest a change in extinction risk, with the notable exception discussed below regarding the Carmel River.

However, there is new information on genetics and the methodology relevant to viability criteria.

Below we present a discussion of these topics, followed by an up-dated summary of current monitoring efforts and results (Boughton in Williams et al. 2016).

Risk status is based on the concept of viability at two levels of organization: the overall DPS, and individual populations composing the ESU of which the DPS is part.

2.3.1.1 DPS Viability
The South-Central California Steelhead Recovery Plan (National Marine Fisheries Service 2013) included viability criteria for a set of core populations (Table 5) and incorporated the scientific recommendations by specifying a set of core populations on which to focus the recovery effort, i.e., “Core 1” and “Core 2” populations (Table 5 and Table 6, DPS-Level Criteria, and Figure 4).

Formally, if each of these core populations were restored to viability (Table 6, Population-Level Criteria), and they also meet DPS-level criteria (Table 6, DPS-Level Criteria), the DPS as a whole would be considered viable from a scientific perspective (Boughton et al. 2007). 13 Table 5. Monitoring status in Core 1 and 2 populations designated by South-Central California Steelhead Recovery Plan for recovering to viability.

POPULATION ADULT SPATIAL SMOLT
ABUNDANCE? STRUCTURE? COUNTS?
South-Central California Coast DPS
Interior Coast Range populations
Pajaro River N I N
Salinas River pops. Y I B
Carmel River population
Carmel River B I N
Big Sur Coast populations
San Jose Creek N N N
Little Sur River N N N
Big Sur River B* N N
San Luis Obispo Terrace
San Simeon Creek N N N
Santa Rosa Creek N N N
San Luis Obispo Creek B* N N
Pismo Creek N N N
Arroyo Grande Creek N N N
Y = yes, N = No, B = estimates are likely biased (B* = redd counts, which can be bias-corrected with data from lifecycle monitoring stations), I = index reaches rather than randomly sampled reaches or complete census of anadromous habitat.
14 royo de la Cruz
• City
River/ Stream
CJ South-Central California Steelhead
Recovery Planning Area
High Priority Core Recovery Populations
,.
o
~
A 2s
Miles
Figure 4. High priority core recovery populations in the South-Central California Coast Steelhead DPS.
15 NOAA’s Technical Review Team (TRT) for the South-Central California Coast Steelhead Recovery Planning Area emphasized that core populations be situated in watersheds with drought refugia (Table 6, DPS-Level Criteria). There does not appear to be any systematic information on the distribution of drought refugia, even though the current drought provides a valuable opportunity to identify such refugia. Thus it is unclear if the selected set of core populations meets this criterion.

The viability report developed for the South-Central California Coast Steelhead Recovery Planning Area noted that “. . . tree-ring data described by Cook et al. (2004) go back to the year 800 A.D., and record at least 4 multi-decade droughts prior to 1300 A.D. These events had far greater magnitudes than anything observed during the historical period. The aboriginal steelhead populations must have either survived in drought-resilient refugia, or have been regionally extirpated prior to 1300 A.D. and recolonized in the subsequent centuries. If the refugium hypothesis is correct, ESU viability is probably contingent on forecasting the location of refugia under future climate regimes. If the recolonization hypothesis is correct, ESU/DPS boundaries are currently mis-specified. Evaluation of the refugium hypothesis, particularly as it relates to future climate, is an obvious research priority.” (Boughton et al. 2007, p. 21).

Table 6. Biological Recovery Criteria for the South-Central California Coast Steelhead DPS.

POPULATION-LEVEL CRITERIA: Applies to Populations Selected to Meet DPS-Level Criteria
Criterion
Type1 Recovery Threshold Notes
P.1
Mean Annual
Run Size
Run-size is sufficient
to result in an
extinction risk of < 5%
within 100 years
Monitoring run-size will provide information on
year-to year fluctuations in the population
necessary to determining the appropriate recovery
threshold for individual populations. Research on
the role of non-anadromous spawning fraction in
stabilizing anadromous faction will also enable
refinement of the minimum recovery threshold
(see Boughton et al. [2007] for discussion of
steps in determination of threshold value for each
viable population)
P.2
Ocean
Conditions
Run-Size criterion met
during poor ocean
conditions
“Poor ocean conditions” determined empirically,
or size criterion met for at least 6 decades
P.3
Spawner
Density
Unknown at present Research needed
P.4
Anadromous2
Fraction
N = 100% of Mean
Annual Run-Size Requires further research
16 DPS-LEVEL CRITERIA
Criterion
Type Recovery Threshold
D.1
Biogeographic
Diversity

1. Biogeographic Population Group contains minimum number of viable populations:

Interior Coast Range: 4 populations
Carmel River Basin: 1 population
Big Sur Coast: 3 populations
San Luis Obispo Terrace: 5 populations
Viable populations inhabit watersheds with drought refugia

2. Viable populations separated from one another by at least 42 miles or as widely dispersed as possible3
D.2
Life-History
Diversity
All three life-history types (fluvial-anadromous, lagoon-anadromous, freshwater resident) are exhibited and distributed across each Biogeographic Population Group
1 It is assumed that all spawner criteria represent escapement (i.e., un-harvested spawning adults) rather than migrating adults that may be captured before having an opportunity spawn. 2 The anadromous fraction is the percentage of the run-size that must exhibit an anadromous life-history to be counted toward meeting the mean annual run-size criteria. However, the recovery strategy recognizes the potential role of the non-anadromous form of O. mykiss and includes recovery actions which would restore habitat occupied by the non-anadromous form, as well as reconnect such habitat with anadromous waters, and thus allow the anadromous and non-anadromous forms to interbreed, and the non- anadromous forms to potentially express an anadromous life-history. 3 This geographic separation is based on the maximum width of recorded historic wildfires.

2.3.1.2 Population Viability
Viability criteria at the population level are summarized in Table 6. There was broad agreement among the TRT that the viability metrics of Table 6 were sufficient for assessing risk, but also agreement that the specific viability criteria were highly sensitive to scientific uncertainty about key aspects of steelhead ecology (Boughton et al. 2007). These key knowledge gaps included 1) uncertainty about the magnitude of normal fluctuations in adult abundance, and 2) uncertainty about the underlying biological mechanisms for expression of life-history diversity, especially factors triggering anadromous versus resident life-histories within populations. Thus the criteria that mean annual spawner abundance 1) be greater than 4,150, and 2) be composed of 100% anadromous individuals, were recommended as a risk-averse approach. It was expected that further scientific work would either support these criteria or allow one or both to be relaxed, depending on results.

NMFS convened a research and monitoring colloquium in 2014 at the National Center for Ecological Synthesis and Analysis (NCEAS). The participants identified several key areas of research, including: 1) the functional basis for partial migration of O. mykiss; 2) habitat structure and its relationship to life-history strategies; 3) the assessment of nursery habitats, including mainstem, intermittent stream reaches, and estuaries; 4) interactions with non-native species, including predation and disease; and 5) the general ecology of the marine phase of O. mykiss.

The group elected to work on the first four of these topics, by producing white papers further refining the research needs and approaches to carrying out this research. The last five years have 17 seen little progress in developing better scientific information on population fluctuations, but significant progress on maintenance of life-history diversity. However, there has been no work on how the ecological and biological factors that maintain life-history diversity at the population level bear on the viability criterion for the anadromous fraction of the O. mykiss complex.

Data on population fluctuations will emerge over time with the implementation of the California Coastal Monitoring Plan (CMP), discussed further in the next section. The California CMP emphasizes annual estimates of abundance of anadromous adults in each Core 1 and Core 2 population, which is intended to provide data on abundance and productivity metrics, including abundance fluctuations. Missing from the California CMP, but just as important with respect to any future revision of viability criteria, are ongoing monitoring of abundance and fluctuations of the resident life-history type in each population over time, and the lagoon-anadromous form (Boughton et al. 2007).

2.3.1.3 Maintenance of life-history diversity
Previous research led by NMFS and UC Santa Cruz suggested that diversity of life-histories (anadromous versus resident life-histories, diversity in age of smolting and age of maturation) was largely controlled by diversity in growth rates during the early life-history of the fish (Satterthwaite et al. 2012, 2009, Beakes et al. 2010, Bond et al. 2008), and thus was largely under ecological control. On the other hand, numerous studies have demonstrated the heritability and genetic influence on expression of anadromy (Kendall et al. 2015). In particular, a recent analysis identified an important genetic component on chromosome Omy5 (Pearse et al. In review, Pearse et al. 2014, Martinez et al. 2011). Evidently, a portion of O. mykiss chromosome 5 has undergone an inversion, in which a segment of the chromosome has been reversed end to end in some fish but not others. This presumed inversion is passed on to progeny, but for fish in which one chromosome is inverted and the other not (i.e., a parent of each type), no crossingover can occur during meiosis, (double cell division producing four cells – sperm in males, eggs in females - containing half the original amount of genetic material) and so the set of genes on the inverted section of chromosome are tightly linked (i.e., prevented from mixing between the two chromosome types). Such tightly linked sets of genes are sometimes called “supergenes.” Pearse et al. (2014) surveyed the occurrence of these two chromosome types in existing genetic samples from throughout the California coastal mountains, and found several interesting patterns:
1) Both chromosome types were present at most sites;
2) There was strong evidence of selection on the set of linked genes within the inversion; and
3) One chromosome type dominated sites in anadromous waters, whereas the other chromosome type dominated sites in formerly anadromous waters that are now upstream of impassable dams (a notable exception is the adfluvial population in the upper Arroyo Grande Creek above Lopez Dam where the population contains a high frequency of the chromosome type associated with anadromy).

Pearse et al. (2014) concluded that natural selection favors one chromosome type in anadromous waters, and this chromosome type, therefore, likely plays a role in maintaining the anadromous life-history, and natural selection favors the other chromosome type in non-anadromous waters, 18 and, therefore, likely plays a role in maintaining the resident life-history. However, both chromosome types do occur in both types of waters, and both life-histories are observed in anadromous waters, so the relationship is probably not a simple association between resident and anadromous genomic elements.

Pearse et al. (In review) combined genetic analysis of the Omy5 inversion with a mark-recapture study of juvenile O. mykiss in a small population in the Big Sur BPG (in the neighboring SouthCentral California Coast Steelhead DPS). For age 0 fish, the probability of emigrating from freshwater to the ocean was associated with chromosome type, sex, and juvenile body size, and also interaction effects for these three traits. However, the associations were probabilistic rather than “complete”: emigrants included juveniles of both sexes, a broad range of sizes (100 – 250 mm), and both chromosome types. Pearse et al. (In review) conclude that the Omy5 inversion region represents a “supergene with a major effect on a complex behavioral trait [i.e., migration],” but that the individual component genes have not yet been resolved, and also that chromosome Omy12 “also contains regions important for smoltification-related traits . . . In addition, other genomic regions, heritable epigenetic effects, and subtle population structure or assortative mating may also affect this complex life-history trait.” Rundio et al. (2012) also described evidence that females were more likely than males to emigrate in this study population, and Ohms et al. (2014) documented similar female-biased emigration in 9 populations distributed broadly across the Pacific Northwest, southern Alaska, and northern California.

These new findings demonstrate that resident and anadromous life-histories in O. mykiss in the South-Central/Southern California Coast Steelhead Recovery Planning Domain and elsewhere are tightly integrated. This in turn suggests that the viability criterion for a 100% anadromous fraction in core populations (Table 6, Population-Level Criteria) should be revised. However, the studies summarized above do not include any population-viability analyses, which would be necessary for proposing a specific revision of the criterion.

2.3.1.4 New information on methodology for viability metrics California’s (CMP) draws on the Viable Salmonid Population (VSP) framework of McElhany et al. (2000) to assess viability in terms of four population metrics: abundance, productivity, spatial structure and diversity. The California CMP also outlines the creation of a system of Life-Cycle Monitoring (LCM) stations to collect additional data necessary for the interpretation of those four metrics (Adams et al. 2011). The California CMP is intended to provide data sufficient to conduct status reviews under the ESA, but at present is only partially implemented. Here we review methodological issues that appear to be impeding implementation; in section 2.3.1.4.2 we review the level of implementation thus far within the South-Central California Coast Steelhead DPS.

According to Adams et al. (2011), the California CMP divides the coastal zone of California into northern (Santa Cruz to California-Oregon border) and southern (Monterey to U.S.-Mexico border) areas based on differences in species composition, levels of abundance, distribution patterns, and habitat differences that require distinct monitoring approaches. The South-Central and Southern California Coast Steelhead DPSs are in the southern area. Implementation of the California CMP in the southern area involves monitoring the following metrics in the core populations listed in Table 5 (Adams et al. 2011):
19 1) Unbiased estimates of annual anadromous run-size, for tracking abundance and productivity;
2) Unbiased estimates of the spatial distribution of juveniles, possibly also in lower priority populations, for tracking spatial structure;
3) Unbiased estimates of annual smolt production in a subset of Table 5 populations that are well-distributed biogeographically (LCM stations), for distinguishing between changes in ocean conditions and freshwater conditions; and
4) Unbiased estimates of diversity metrics, still to be determined, for tracking diversity.

Here, “unbiased” is used in the statistical sense of estimators whose long-run sampling distribution is equal to the parameter being estimated—for example, methods that do not systematically undercount or over count fish across repeated surveys. Below we summarize methodological progress on estimating these four metrics.

2.3.1.4 (a) Abundance and Productivity
In both northern and southern California CMP monitoring areas, the assessment of abundance and productivity is based upon unbiased estimates of the annual number of anadromous adults across each ESU/DPS, with productivity calculated as the trend in anadromous adults over time.

In the northern California CMP monitoring area adult abundance is estimated via redd surveys conducted in a spatially balanced, stratified-random sample of stream reaches, and bias-corrected by redds-per-female estimates obtained from life-cycle monitoring stations. At the time of California CMP development, redd surveys were believed to be infeasible in the southern area due to the extremely episodic flow regime and high bed loads (movement of sand and gravel) during the spawning season, as well as the inaccessibility of many upland tributaries during the rainy season. Instead the California CMP specified that abundance be estimated by counting upstream migrants at fixed counting stations in the lower mainstems of rivers, but was somewhat agnostic about how it would be done.

To fully support a status review update such as this one, such counting would need to occur in the full complement of populations listed in Table 5. However, counting would not necessarily need to occur in every population in every year; a rotating-panel sampling plan could probably be used, similar to the sampling of reaches used for redd surveys in the northern area, but with sampling units being whole populations rather than individual stream reaches. That is, some of the populations in Table 5 would be counted every year, others would be counted every 3 or 4 or 12 years on a staggered schedule. This is not something envisioned in the original California CMP, but would be consistent with its goals and more efficient to implement.

Since the development of the California CMP strategy outlined in Adams et al. (2011), there appear to have been two efforts to conduct redd surveys in the southern area, with mixed results.

The Monterey Peninsula Water Management District has conducted redd surveys in the lower Carmel River as District resources have permitted, but could not fully implement the protocols used in the northern area (e.g., Gallagher and Gallagher 2005). These protocols specify that sampled reaches be surveyed every two weeks for the duration of the spawning season, and this was not possible in the lower Carmel due to high flows associated with the episodic flow regime, 20 probably leading to an undercount of redds (Kevan Urquhart, Monterey Peninsula Water Management District, personal communication 2015). On the other hand, the NMFS California Coastal office in Long Beach has had success conducting redd surveys in the Ventura River and Malibu Creek (in the adjacent Southern California Coast Steelhead DPS) that adhere closely to the northern area protocol, though these data have not been continued for sufficiently long to support a status assessment (Richard Bush, National Marine Fisheries Service, personal communication 2015, Bush and Spina 2011).

These efforts suggest that redd surveys might be able to produce unbiased estimates of adult abundance in certain situations but not others. In situations where they appear feasible, such as the Carmel River system, redd surveys would need to be bias-corrected using estimates of reddsper-female estimated at LCM stations (Adams et al. 2011). If redd surveys were to become a strategy for implementing the California CMP in the southern area, they would probably not be a universal solution as in the north. The problem with sampling during high flows is also encountered in the northern area (Dana McCanne, California Department of Fish and Wildlife, personal communication 2015). The problem with sampling in inaccessible mountain tributaries during the rainy season has not yet been addressed.

At the time of California CMP development, one of the most promising methods for counting anadromous adults was the new DIDSON acoustic camera (Pipal et al. 2012, Pipal et al. 2010a, Pipal et al. 2010b). These have started to be deployed in the South-Central/Southern California Coast Steelhead Recovery Planning Domain; currently in the Carmel River, as well as further south in the Southern California Coast Steelhead DPS: Ventura River, Carpinteria Creek and Salsipuedes Creek (tributary of Santa Ynez River). There appear to be three problematic methodological issues. The most important is that in some situations, upstream migrating steelhead frequently drift or swim back and forth across the front of the camera. As a result, a single upstream migrant can be counted as multiple individual fish moving in the up and downstream direction (Monterey Peninsula Water Management District 2014). As an example of the estimation problems this behavior poses, if significant numbers of adult steelhead survive spawning, and migrate downstream to the ocean as kelts, then accurate counts of kelts and upstream adults would be confounded, leading to biased estimates. Two other methodological issues are species identification and the sheer number of person-hours required to review DIDSON output in order to reliably produce accurate counts. The latter issue should be amenable to improvement by using machine-learning techniques to aid in image interpretation.

This is a promising avenue for research that might lead to cheaper, more efficient DIDSON monitoring.

Various other methods have been or are starting to be used to count anadromous adults, such as monthly snorkel surveys in Topanga Creek (Dagit 2016, Stillwater-Sciences et al. 2010, Dagit et al. 2009), trapping stations in tributaries of the Santa Ynez River (Robinson et al. 2009), a visual imaging system at a fish passage facility on the Salinas River (Cuthbert et al. 2014a), and a counter on a fish ladder on the Carmel River (Monterey Peninsula Water Management District 2013). In addition, a method has been proposed to use two-stage sampling and PIT(Passive Integrated Transponders)-tagging of juveniles combined with monitoring of migrants (Boughton 2010b). We summarize data from these sources and methodological issues later in this section, and in the update on the status of the South-Central California Coast Steelhead DPS below in section 2.3.1.4.2. The most important methodological issues appear to be 1) the need to consistently provide unbiased estimates of adult abundance, for example by estimating 21 observation or capture probabilities and by use of randomly sampled stream reaches rather than subjectively chosen index reaches; and 2) the need for methods suitable for the normal range of environmental conditions expected for the domain, which typically involve extreme flow events, high bed loads, and remote rivers and tributaries that are difficult to access during the wet season.

2.3.1.4 (b) Spatial Structure
The California CMP recommends that spatial structure be monitored using summer and fall snorkel surveys that count juveniles in a stratified-random, spatially balanced sample of reaches (Adams et al. 2011). The sampling is achieved using Generalized Random Tessellation Stratified (GRTS) sampling to achieve spatial balance, and a rotating panel design to achieve a balance between the need to estimate structure at a particular time, and the need to estimate trends in structure over time. This is the same sampling framework used in the northern California CMP area for both red surveys and juvenile surveys.

To our knowledge, no such data have been collected in the South-Central California Coast Steelhead DPS in the last 5 years, and no broad-scale data using reach-sampling have been produced. However, the California Department of Fish and Wildlife (CDFW) is in the process of developing a ground-truthed sampling frame for Monterey County (Jennifer Nelson, California Department of Fish and Wildlife, personal communication 2015).

2.3.1.4 (c) Diversity
At the time of California CMP development, diversity traits were not sufficiently understood for their monitoring to be specified. Adams et al. (2011) stated that “local diversity traits will need to be surveyed, eventually leading to local diversity monitoring plans. Specific projects targeting both broad and focused levels and patterns of genetic diversity will be developed. Tissue collections for these projects will be coordinated with other California CMP activities.” We are now in a better position to propose some diversity traits that need to be monitored to assess viability. The viability criteria (Table 6, see also Boughton et al. (2007) emphasize the critical importance of resident adults. The findings of Adadia-Cardoso et al. 2016, Pearse et al. (2014) and Jacobson et al. (2014) show the importance of genetic information for assessing viability, both in terms of genetic heritage (e.g., native vs. hatchery introductions) and in terms of occurrence of the supergene variants.

Diversity metrics in the form of unbiased estimates of resident adults and the distribution and diversity of genetic polymorphisms could all be integrated in a straightforward manner with the broad-scale juvenile sampling that the California CMP specifies for spatial structure. An important methodological change would be required: Collection of genetic samples requires handling the fish, which means that mark-recapture or depletion electrofishing would need to occur at a subsample of the reaches selected for juvenile snorkel counts. Such subsampling would also allow the snorkel counts to be bias-corrected (Boughton et al. 2009). If methods were developed to distinguish juveniles from resident adults in both snorkel counts and electrofishing samples, an unbiased estimate could then be made of the number of resident adults in the sampling domain. Additionally, tissues could be taken from electrofishing sites for genetic analysis that would provide unbiased estimates of various gene frequencies. It is important that the California CMP be updated to include such diversity monitoring. 22 Environmental DNA (eDNA) is an emerging surveillance tool to monitor the genetic presence of an aquatic species; it might provide another avenue for monitoring genetic diversity, but its statistical properties for inferring unbiased gene frequencies in the steelhead population is unclear.

2.3.1.4.1 Life-Cycle Monitoring Stations
According to Adams et al. (2011), LCM stations are a fundamental component of the California CMP that perform two functions: providing unbiased estimates of ocean survival so that changes in salmonid numbers can be parsed into changes due to freshwater versus marine conditions; and as “magnets for other kinds of recovery-oriented research, particularly studies of fish habitatproductivity relationships and evaluations of habitat restoration effectiveness.” For the first function (estimating marine survival), an LCM station needs three attributes: 1) annual, unbiased estimates of anadromous adults, 2) annual, unbiased estimates of smolt production, and 3) sufficiently large number of anadromous adults to provide accurate estimates of marine survival (at least 20 per year, preferably more than 100 anadromous adults each year).

Methodological issues for estimating anadromous adults were described above in the section on abundance and productivity.

Methodological issues for estimating smolt production have seen little progress since the last status review (2010) and remain problematic. Originally the DIDSON acoustic camera seemed promising as a tool for estimating smolt production, but the size of smolts is close enough to the resolution of DIDSON imagery that detection probability is likely substantially less than 1 (Kerrie Pipal, NOAA Southwest Fisheries Science Center, Santa Cruz Laboratory, personal communication 2015). Fyke nets, traps, and visual imagery at fish passage facilities, developed for counting anadromous adults, are also being used to count smolts, but with qualified success.

The main problem is counts that are likely biased low due to failure of counting stations during high flow events. Two other problems are distinguishing smolts from juvenile downstream migrants (typically age-0 or age-1 fish moving down to the estuary near the end of smolting season and in early summer), and the difficulty of estimating smolt body sizes. Although estimates of smolt body sizes were not emphasized in the California CMP, we should expect marine survival to involve strong interaction effects between ocean condition and smolt sizes at ocean entry (Ward 2000, Bond 2006). If this were not accounted for then some unknown component of change in marine survival may instead be due to changes in freshwater conditions via its effect on smolt body size.

Boughton (2010b) described a framework for using PIT tags to estimate both smolt production and adult abundance. PIT tags would be implanted in juveniles sampled from reaches sampled from a stream network, and thus would be straightforward to integrate with the reach-sampling methods used for spatial structure (described above). Smolt production is estimated from the proportion of tagged fish that are detected at a downstream tag-reading station near the mouth of the river. An application of this approach in the South-Central/Southern California Coast Steelhead Recovery Planning Domain has not yet been described, but some advantages and disadvantages are already clear. Advantages are that the method could be integrated with spatialstructure sampling; could provide information on smolt size (via pre-smolt size at the time of sampling); and since the originating reaches of tagged smolts would be known, it could provide a powerful tool for evaluating habitat-productivity relationships, including testing of various 23 habitat-restoration actions, regulatory actions, or flow-management actions relative to “control” reaches. Disadvantages are that progress is still needed for designing reader stations (particularly antennae) that are robust in high-flow events, and that over time this approach is likely to lead to an accumulation of tags in the river bed (from dead juveniles) (David Rundio, NOAA Southwest Fisheries Science Center, Santa Cruz Laboratory, personal communication 2015). These “ghost tags” get moved by high-flow events and cannot be readily distinguished from live smolts, thus generating overestimates of smolt production. The bias would tend to increase over time as tags accumulate, such that the ghost tags would generate a “ghost recovery” of smolt production.

2.3.1.4.2 Summary of viability metrics currently collected in the South-Central California Coast Steelhead Recovery Planning Area
The following provides a summary of the viability metrics that are currently being collected within the South-Central California Coast Steelhead Recovery Planning Area from those few watersheds where monitoring has occurred (Williams et al. 2016). In general the metrics are not formally assessed because the period of record is too short for such an assessment to be meaningful. See Figure 5 for general location of annual/periodic monitoring. 24 ~
A 2s
Miles
e Annual/Periodic Monitoring
e City
.../'v- River /Stream
11 South-Central California Steelhead
L.......J Recovery Planning Area
C:=J High Priority Core Recovery Populations
Figure 5. Annual or periodic monitoring or surveying within the South-Central California Coast DPS.
25 Interior Coast Range BPG
Pajaro River
No adult counts or smolt counts have been made in the Pajaro River (Core 1 population). The City of Watsonville has installed a fish ladder on Corralitos Creek which is equipped with a video camera with night infra-red capability (Figure 6). The city has recorded several terabytes of data in past years (2009 to the present), but no real video analysis has done. No adults have been found in the adult ladder, and only a handful of juvenile steelhead have ever been found in the juvenile ladder in any given year. (Gary Kittleson, Kittleson Environmental Consulting, personal communication 2016, Kittleson 2010, 2009). The organization Coastal Habitat Education and Environmental Restoration (CHEER) has rescued a mean of 12 adult steelhead per year (sd = 20) from 2006 through 2013 (Joel Casagrande, National Marine Fisheries Service, personal communication 2015), suggesting consistent occurrence of at least modest numbers of anadromous fish. Some limited assessments of spatial structure have been made in Uvas Creek, Llagas Creek and Corralitos Creek since 2005, using backpack electrofishing at index reaches, and annual juvenile steelhead distribution and abundance surveys and informal adult observations in Uvas Creek for the past 11 years (Casagrande 2016, 2015, 2014, 2013, 2012, 2011). Surveys of juvenile densities in four sites within Corralitos Creek have also been conducted annually since 2006, along with surveys in the Pajaro River estuary (D. W. Alley & Associates 2015a, 2015b, 2013), but there do not appear to be unbiased estimates of spatial structure based on stratified-random sampling.
26 A B
Figure. 6. Fish Passage Facilities, Corralitos Creek, Pajaro River. Photo courtesy Kittleson Environmental Consulting. A – Juvenile fish passage. B – Adult fish passage.

Salinas River
The Salinas River (Core 1 population, comprised of 3 sub-populations) has an established counting station in operation since 2011 (Figure 7), but counts have only been made for three years: 2011, 2012, and 2013 (Joyce Ambrosius, National Marine Fisheries Service, personal communication 2016). Cuthbert et al. (2014a) reported a mean of 22 (sd = 22) total upstream migrants per year. Also reported are net upstream migrants (total upstream migrants minus total downstream migrants) with a mean of 18 (sd = 18) migrants per year. Smolt production has also been monitored with rotary screw traps since 2010, but the counts are likely biased low due to incomplete coverage of the migration season and low (unquantified) trap efficiency during some flow conditions (Cuthbert et al. 2014b).

Juvenile abundance has been estimated via backback electrofishing at eight index reaches since 2010 (Monterey County Water Resources Agency 2014a). Adult steelhead escapement and juvenile O. mykiss downstream migration has monitored with downstream Fyke-net and screw traps (Monterey County Water Resources Agency 2014b, 2014c. 2014d, and 2014e; see also Monterey County Water Resources Agency 2014f, 2013, 2012, and 2011). In 2014 and 2015 the mouth did not open or river reaches were dry due to the drought so no adult entered the river (Joyce Ambrosius, National Marine Fisheries Service, personal communication 2016). There do not appear to be unbiased estimates of spatial structure based on stratified-random sampling. 27 B
A
Figure 7. Adult Steelhead Escapement Monitoring, lower Salinas River. Photo courtesy Monterey County Water Resources Agency. A – Weir. A – Trap entrance, looking downstream.

Carmel River Basin BPG
Carmel River
The Carmel River (Core 1 population) is the only population within the domain for which there is a time-series of adult abundance longer than 20 years. Unfortunately the counts probably have a bias that has changed over time, because the counting has occurred at San Clemente Dam and misses any adults that spawn in the river downstream of the dam. This downstream area has been an area of extensive habitat restoration in the past 15 years, so the number of fish spawning here has likely increased and thus the negative (undercount) bias in the counts has probably also increased over time (Kevan Urquhart, Monterey Peninsula Water Management District, personal communication 2015).

A plot of the counts (Figure 8) shows interesting variation over time. A period of zero counts from 1988 to 1991 were due to a drought, during which local water users drew down the water table and the lower river remained continuously dry and offered no opportunities for migration.

During this period the Carmel River Steelhead Association used a nearby seawater facility to 28 operate a broodstock program, releasing many mature anadromous adults as well as hundreds of thousands of juveniles to the river system (Thomas 1996). Numbers quickly climbed after the end of the drought (and the broodstock program) in 1991. 0 0
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Figure 8. Adult steelhead counted at San Clemente Dam on the Carmel River at river mile

18.6 of the Carmel River since 1988.

The past 20 years (1996–2015) has seen a consistent though irregular decline in numbers (Figure 8), with an average decline of 16.5% per year (or about 50% per generation, assuming a 4-year generation time). Low counts in 2014–2015 are almost certainly due to drought, but the decline was clearly underway prior to 2014.

The 20-year decline coincides with a period of intense management aimed at recovering steelhead, including a restoration of estuary habitat, restoration of riparian vegetation, partial restoration of water tables, and a captive-rearing program for juveniles that get stranded in drying sections of river during the summer. One possible explanation for the decline is that improved conditions in the lower river motivate many adults to stop and spawn prior to reaching the dam and getting counted. However, the local water district, Monterey Peninsula Water Management District (MPWMD) has conducted occasional redd surveys, and found that the number of redds downstream of the dam do not fully account for the decline (see previous status review update, Williams et al. 2011). This suggests the recorded decline is quite real, not an artifact of monitoring practices.

Arriaza (In review) describes the application of a life-cycle model to steelhead data in the Carmel River. The analysis suggests the decline is due to a long-term decline in the growth rates of age-0 juveniles in the river, which reduces the smolting rate and the survival of smolts once 29 11 June 2015 8 December 2015
they enter the ocean. The decline in growth rates has apparently led to a switch from most anadromous adults being the result of in-river wild production, to most anadromous adults being fish released from the Sleepy Hollow Rearing Facility. From 2005 onward, the vast majority of production of anadromous adults appears to have come from the rearing facility (Arriaza, In review, see Figure 2).

A B
Figure 9. San Clemente Dam site. A and B – Before (L) and after (R) removal of San Clemente Dam. Photo courtesy Thomas. W. Williams, NOAA Southwest Fisheries Science Center, Santa Cruz Laboratory.

A notable restoration event in the Carmel River during the past 5 years has been the recent removal of San Clemente Dam, and the rerouting of the river channel around the large stockpile of sediment that had accumulated in the dam over the past 90 years. Removal of the dam and rerouting the river have been completed in time for the 2016 water year, which commences 1 October 2015 (Figure 9). The ecological effects of the dam removal on downstream habitats and on steelhead population viability are the subject of on-going monitoring and investigation (Thomas W. Williams, NOAA Fisheries Southwest Science Center, Santa Cruz Laboratory, personal communication 2015).

Big Sur Coast BPG
San Jose Creek
There is no apparent monitoring of viability metrics in San Jose Creek (Core 1 population).

Big Creek
NOAA’s Southwest Fisheries Science Center, Santa Cruz Laboratory has conducted a PIT tagging study of steelhead in Big Creek (Core 3 population) since 2004, but to date has not used 30 the study to estimate abundance of anadromous adults, spatial structure of juveniles, or smolt production. See Figure 10.

A
B
Figure. 10. PIT tagging study, Big Creek. A and B – Antenna array. Photo courtesy Thomas W. Williams, NOAA Southwest Fisheries Science Center, Santa Cruz Laboratory.

Little Sur River
There is no apparent monitoring of viability metrics in Little Sur River (Core 1 population).

Big Sur River
CDFW has conducted redd surveys in the Big Sur River (Core 1 population) in 2012 (first field test) and in the 2014 and 2015 spawning seasons (Jennifer Nelson, California Department of Fish and Wildlife, personal communication 2015). Each year they surveyed the entire anadromous portion of the stream network, using the field protocols established by Gallagher and Gallagher (2005) (Patricia Anderson, California Department of Fish and Wildlife, personal communication 2015). Snorkel surveys of juveniles were conducted in 2011 to provide a snapshot of spatial distribution, but have not been continued. Investigation is underway for installation of a DIDSON monitoring site, data from which would provide a basis for estimating redds per female, one of the functions of a life-cycle monitoring station. 31 San Luis Obispo Terrace BPG
San Simeon Creek
There is no apparent monitoring of viability metrics in San Simeon Creek (Core 1 population).

Santa Rosa Creek
There is no apparent monitoring of viability metrics in Santa Rosa Creek (Core 1 population).

Morro Bay Watershed (Chorro, Dairy, Los Osos, Pennington, San Bernardo Creeks) There is no apparent monitoring of viability metrics in the tributaries to the Morro Bay Estuary.

Fish and habitat surveys are periodically conducted in several of the tributaries, but none have been conducted annually, or using protocols identified in the California CMP (California Conservation Corps 2013a, 2013b, 2013c, 2012a, 2012b, 2012c, 2010).

San Luis Obispo Creek
The City of San Luis Obispo initiated redd surveys in 2015 in San Luis Obispo Creek (Core 1 population), and plans to continue the effort using field protocols developed in the Ventura River by NMFS Long Beach Office (Fred Otte, City of San Luis Obispo, personal communication 2015).

Pismo Creek
There is no apparent monitoring of viability metrics in Pismo Creek (Core 1 population).

Fish surveys are periodically conducted in portions of Pismo Creek using a variety of techniques (snorkeling and electrofishing) but have not been conducted annually, or using protocols identified in the California CMP (California Conservation Corps 2012, California Department of Fish and Wildlife 2011).

Arroyo Grande Creek
There is no apparent monitoring of viability metrics in Arroyo Grande Creek (Core 1 population).

Fish surveys have been conducted in lower Arroyo Grande Creek and the lagoon annually since 2009 using a variety of techniques (snorkeling, seining, and electrofishing), but have not used protocols identified in the California CMP (Rischbieter 2015, 2014, 2013, 2012, 2011, 2010, Rischbieter et al. 2015, Swanson Hydrology and Geomorphology 2008). 32 Discussion
The data summarized in this status review indicate small (generally <10 fish) but surprisingly persistent annual runs of anadromous O. mykiss are currently being monitored across a limited but diverse set of basins within the range of this DPS, but interrupted in years when the mouth of the coastal estuaries fail to open to the ocean due to low flows (Williams et al. 2016, Williams et al. 2011).

The question raised by these observations is: How can such small runs of anadromous O. mykiss (in many cases single digits) persist, even over the short term (1 decade)? As noted in the previous status review (Williams et al. 2011), these small runs could be maintained either by natural dispersal from some source population located elsewhere and/or from the consistent production of smolts by the local population of freshwater non-anadromous O. mykiss, including O. mykiss populations currently residing upstream of introduced longstanding barriers to upstream migration (National Marine Fisheries Service 2013).

Genetic assignment tests can be used to assess the likelihood that anadromous fish are strays from other basins. In one such test in the DPS immediately south of the South-Central California Steelhead DPS, of the 16 anadromous fish captured in the Santa Ynez River system in 2008, data from tissue samples assigned 6 (38%) to origins outside the basin, and 10 to origins within the basin (Tim Robinson, Cachuma Operations and Maintenance Board, personal communication 2010, Garza and Clemento 2007). The broader-scale study of Clemento et al. (2009) tended to indicate that populations in different basins are linked by frequent straying, although “frequent” should be understood here in a genetic sense rather than a demographic sense: frequent enough so that family structure dominated the genetic distinctions among basins.

There is a variety of anecdotal evidence that freshwater resident populations of O. mykiss can produce smolts (reviewed in previous status reviews and TRT reports; Beakes et al. 2010). Size and growth rates may provide valuable information as to whether the anadromous or freshwaterresident strategy would provide greater reproductive potential. If this model is generally applicable, then fish with this plastic life-history strategy should generally outcompete either a purely resident or purely anadromous strategy over the long term. However, conditions particular to a given basin and time period may select for a pure strategy in the short term. One would expect that if such a situation persisted long enough, the ability to express the plastic lifehistory strategy would become vestigial, like the eyes of cave-dwelling fish. This has yet to be empirically demonstrated in O. mykiss.

2.3.2 Five-Factor Analysis (threats, conservation measures, and regulatory mechanisms)

2.3.2.1 Present or threatened destruction, modification or curtailment of its habitat or range
South-Central California steelhead have declined in large part as a result of agriculture, mining, and urbanization activities that has resulted in the loss, degradation, simplification, and fragmentation of habitat (Hunt & Associates 2008).
33 Water storage, withdrawal, conveyance, and diversions for agriculture, flood control, domestic, and hydropower purposes have greatly reduced or eliminated historically accessible steelhead habitat. Modification of natural flow regimes by dams and other water-control structures have resulted in increased water temperatures, changes in fish community structures, depleted flow necessary for migration, spawning, rearing, flushing of sediments from spawning gravels, and reduced gravel recruitment. The substantial increase of impermeable surfaces as a result of urbanization (including roads) has also altered the natural flow regimes of rivers and streams, particularly in the lower reaches.

In addition to these indirect effects these development activities have increased direct mortality of adult and juvenile steelhead. Land-use activities associated with urban development, mining, agriculture, ranching, and recreation have significantly altered steelhead habitat quantity and quality. Associated impacts of these activities include: alteration of stream bank and channel morphology; alteration of ambient stream water temperatures; degradation of water quality; elimination of spawning and rearing habitats; fragmentation of available habitats; elimination of downstream recruitment of spawning gravels and large woody debris; removal of riparian vegetation resulting in increased stream bank erosion; and increased fine sedimentation input into spawning and rearing areas; the net effect is the loss of channel complexity, pool habitat, suitable gravel substrate, and large woody debris.

A significant percentage of estuarine habitats have been lost, particularly in the northern and southern portions of the DPS, where the majority of the wetland habitat historically occurred.

The condition of these remaining wetland habitats is in many cases highly degraded, with many wetland areas at continued risk of loss or further degradation (National Marine Fisheries Service 2013).

Although numerous historically harmful practices have been halted, much of the historical damage remains to be addressed, and the necessary restoration activities will likely require decades. Many of these threats are associated with most of the larger river systems such as the Pajaro, Salinas, and Carmel rivers and Arroyo Grande Creek, and many also apply to the smaller coastal systems such as Morro, San Luis Obispo, and Pismo creeks.

These systemic threats have remained essentially unchanged since the last status review (Williams et al. 2011), though individual, site specific threats may have been reduced or eliminated as a result of conservation actions (e.g., through the removal of small fish passage barriers or the restoration of flows). See Section 2.4.2 below.

2.3.2.2 Overutilization for commercial, recreational, scientific, or educational purposes
Steelhead populations traditionally supported an important recreational fishery throughout their range. Recreational angling for both winter adult steelhead and summer rearing juveniles remains a popular sport in many coastal rivers and streams, but began to decline in the mid1970s. Recreational angling in coastal rivers and streams for native steelhead can add to the mortality of adults (which represent the current generation of brood stock) and juveniles (which represent the future generations of brood stock) and may have contributed to the decline of some 34 naturally small populations but is not considered the principal cause for the decline of the species as a whole. During periods of decreased habitat availability (e.g., drought conditions or summer low flow when fish are concentrated in freshwater habitats), the impacts of recreational fishing or harassment on native anadromous stocks have been heightened (National Marine Fisheries Service 2013).

Despite the listing of the South-Central California Steelhead DPS as threatened under the ESA, recreational angling for O. mykiss continues to be permitted in all coastal drainages in southcentral California (and continues in areas above currently impassible barriers). NMFS has previously concluded that recreational harvest is a limiting factor for South-Central California Steelhead (Busby et al. 1996, Good et al. 2005). Angling for both adults and juveniles in those portions of coastal rivers and streams accessible to anadromous runs from the ocean has been restricted through modification of the CDFW’s angling regulations (i.e., angling only below the first road crossing about the estuary, limited to three days a week, with artificial, single barbless hooks, and catch and release only); however, no Fishery Management and Evaluation Plan has been approved by NMFS and the fisheries are not currently authorized under the ESA (California Department of Fish and Wildlife 2015a).

Ocean harvest of steelhead is extremely rare, and is in particular an insignificant source of mortality for south-central California steelhead. High seas driftnet fisheries in the past may have contributed slightly to a decline of this species in local areas, although steelhead are not targeted in commercial fisheries and reports of incidental catches are rare. Commercial fisheries are not believed to be principally responsible for the large declines in abundance observed along most of the Pacific coast over the past several decades. Sport and commercial harvest of steelhead in the ocean is prohibited by CDFW (California Department of Fish and Wildlife 2015b).

While insufficient data exists to estimate South-Central California steelhead freshwater exploitation rates, these rates are likely relatively low given California’s statewide prohibition of capture and retention of natural-origin steelhead since 1998, and the tightly regulated and limited sport fishery within this DPS. Fishing effort estimates based on angler self-report cards are available for 1993–2014 which suggest extremely low levels of effort in this DPS over this period (Figure 11). Although fishing effort estimates for more recent years are not available, there has been no change in the fishing opportunity during this period.

In summary, while there is limited information available on the current level of South-Central California steelhead fishery impacts, it is reasonable to conclude that the level of impact has not appreciably changed since the previous status review in 2010 (Williams et al. 2016, Williams et al. 2011).
35 45.0%

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Percentage of Statewide Angling Effort by Distinct Population Segment for Years 2000-2014
Klamath M tn. Province Central Valley Northern CA Central CA Coast South-Central CA Coast Southern CA California Distinct Population Segment
Figure 11. Distribution of California statewide steelhead fishing effort by DPS for years 2000-2014. California Department of Fish and Wildlife (provisional data).

2.3.2.3 Disease or predation
Infectious disease is one of many factors that can influence adult and juvenile steelhead survival.

Specific diseases such as bacterial kidney disease, Ceratomyxosis, Columnaris, Furunculosis, infectious hematopoietic necrosis, redmouth and black spot disease, Erythrocytic Inclusion Body Syndrome, and whirling disease among others, are present and are known to affect steelhead.

Very little current or historical information exists to quantify changes in infection levels and mortality rates attributable to these diseases for steelhead. Warm water in some cases can contribute to the spread of infectious diseases. However, studies have shown that native fish tend to be less susceptible to pathogens than hatchery cultured and reared fish (Miller et al, 2014, Gilbert and Granath 2003, Buchanan et al. 1983).

Introductions of non-native aquatic species (including fishes and amphibians) and habitat modifications (e.g., dams and impoundments, altered flow regimes, etc.) have resulted in increased predator populations in numerous river systems, thereby increasing the level of predation experienced by native salmonids (Busby et al. 1996). Non-native species, particularly fishes and amphibians such as largemouth and smallmouth bass (Micropterus spp.) and bullfrogs 36 have been introduced and spread widely. These species can prey upon rearing juvenile steelhead (and their conspecific resident forms), compete for living space, cover, and food, and act as vectors for non-native diseases (Cucherousset and Olden 2011).

Artificially induced summer low-flow conditions may also benefit non-native species, exacerbate spread of diseases, and permit increased avian predation; a recent investigation of predation of Western gulls (Larus occidentalis) on juvenile steelhead indicates that modern predation risk is ~2.4 times higher than historically as a result of the increase in gull population due to the increase in artificial feeding opportunities (Osterback et al. 2015). NMFS concluded that the information available on these impacts to steelhead did not suggest that the DPS was in danger of extinction, or likely to become so in the foreseeable future, because of disease or predation. It is recognized, however, that small populations such as south-central California steelhead can be more vulnerable to extinction through the synergistic effects of other threats, and the role of disease or predation may be heightened under conditions of periodic low flows or high temperatures characteristic of south-central California steelhead habitats.

These threats to steelhead in this DPS have remained the same over the previous 5 years, though individual site specific threats may have been reduced or eliminated as a result of conservation actions (e.g., through the restoration of flows or riparian habitats which affect water temperature).

2.3.2.4 Inadequacy of existing regulatory mechanisms
At the time of the original listing of the South-Central California Coast Steelhead in 1997, several Federal regulatory and planning mechanisms affected the conservation of steelhead populations within the DPS. These included: 1) land management practices within those portions of the Los Padres National Forests within the DPS; 2) the regulation of dredging and the placement of fill within the waters of the United States by the U.S. Army Corps of Engineers (USACE) through the Clean Water Act (CWA) Section 404 Program; 3) the regulation of dredging and the placement of fill within the waters of the United States through the CWA section 401 water quality certification regulations; 4) the Federal Emergency Management Agency (FEMA) administration of a Flood Insurance Program which strongly influences the development in waterways and floodplains; and 5) inadequate implementation of the CWA sections 303(d)(1)(C) and (D) to protect beneficial uses associated with aquatic habitats, including fishery resources, particularly with respect to non-point sources of pollution (including increased sedimentation from routine maintenance and emergency flood control activities within the active channel and floodplain).

For example, the USACE program is implemented through the issuance of a variety of Individual, Nationwide and Emergency permits. Permitted activities should not “cause or contribute to significant degradation of the waters of the United States.” A variety of factors, including inadequate staffing, training, and in some cases regulatory limitations on land uses (e.g., agricultural activities) and policy direction, resulted in ineffective protection of aquatic habitats important to migrating, spawning, or rearing steelhead. The deficiencies of the current program are particularly acute during large-scale flooding events, such as those associated with 37 El Niño conditions, which can put additional strain on the administration of the CWA Section 404 and 401programs.

Similarly, FEMAs’ National Flood Insurance Program regulations allow for development in the margins of active waterways if they are protected against 100-year flood events, and do not raise the water elevations within the active channel (floodway) more than one foot during such flood events. This standard does not adequately reflect the dynamic, mobile nature of watercourses in south-central California, and the critical role that margins of active waterways (riparian areas) play in the maintenance of aquatic habitats. In addition, FEMA programs for repairing flood related damages (Public Assistance Program, Individual and Households Program, and Hazard Mitigation Grant Program) promote the replacement of damaged facilities and structures in their original locations, which are prone to repeated damage from future flooding, and thus lead to repeated disturbance of riparian and aquatic habitats important to migrating, spawning, or rearing steelhead.

At the time of listing, several non-Federal regulatory and planning mechanisms also affected the conservation of steelhead populations within the South-Central California Steelhead DPS. These included: 1) administration of the California State Water Resources Control Board (SWRCB) water rights permitting system which controls utilization of waters for beneficial uses throughout the state; 2) state and local government permitting programs for land uses on non-federal and non-state owned lands; 3) administration of the CDFW Code Section 1600 et seq. (Streambed Alteration Agreements) program; and 4) the lack of an updated and completed California CMP to inform regulatory actions such as angling restrictions.

For example, the SWRCB water rights permitting system contains provisions (including public trust provisions) for the protection of instream aquatic resources. However, the system does not provide an explicit regulatory mechanism in the South-Central California Coast Steelhead Recovery Planning Area to implement the CDFW Code Section 5937 requirement for the owner or operator of a dam to protect fish populations below impoundments. Additionally, SWRCB generally lacks the oversight and regulatory authority over groundwater development comparable to surface water developments for out-of-stream beneficial uses, though the passage of the California Sustainable Groundwater Management Act in 2014 partially addresses this inadequacy in some water basins.

The Section 1600 Lake or Streambed Alteration Agreements program is the principal mechanism through which the CDFW provides protection of riparian and aquatic habitats. Inadequate funding, staffing levels, training and administrative support have led to inconsistent implementation of this program, resulting in inadequate protection of riparian and aquatic habitats important to migrating, spawning and rearing steelhead.

The deficiency is governmental regulatory mechanisms is compensated in part in the SouthCentral California Coast Steelhead Recovery Planning Area by local or regional public institutions specifically involved in steelhead recovery planning and implementation. Several special districts (Monterey Peninsula Water Management District, Monterey County Water Resources Agency, San Luis County Water Agency, California Conservation Corps Veterans Green Jobs Program – Los Padres Service District, San Luis/Morro Bay Resource Conservation 38 District), Upper Salinas-Las Tablas Resource Conservation District) have been engaged habitat restoration and modifying infrastructure and operations to address impacts to steelhead in the Carmel, River, Salinas River, Arroyo Grande Creek, and south coast and Morro Bay watersheds.

Notable nongovernmental organizations (NGOs) pursuing steelhead conservation activities include Tri-Counties Fish Team (Ventura, Santa Barbara, and San Luis Obispo counties); the Arroyo Seco River Alliance, Carmel River Steelhead Association, Central Coastal Salmon Enhancement, Coastal Habitat, Education, and Environmental Restoration -CHEER (Pajaro River), Garrapata Creek Watershed Council, Monterey Bay Salmon and Trout Project, The Land Conservancy of San Luis Obispo County, and Upper Salinas Watershed Coalition. Other portions of the Recovery Planning Area are the focus of attention of individuals, groups, or agencies with broader responsibilities or interests. These NGOs are also engaged in public outreach and education initiatives focusing on steelhead and watershed related restoration and management.

Other portions of the Recovery Planning Area are the focus of attention of individuals, groups, or agencies with broader conservation interests or responsibilities.

Monitoring of stocks (particularly annual run-sizes) is essential to assess current and future status of the listed species as well as to develop basic ecological information about listed salmon and steelhead. However, the California CMP has not been updated to take into account new monitoring methodologies and funding for its implementation has not been identified or secured.

See discussion in Section 2.3.1 above and recommendations in Section 4.0 below.

These regulatory mechanisms have not been fundamentally altered in the past 5 years (with the notable exception of the curtailment of angling in anadromous waters and the California Sustainable Groundwater Management Act) and as a consequence the threats to steelhead and its habitat from the inadequacies of regulatory mechanisms has remained essentially unchanged since the last status review (Williams et al. 2011).

2.3.2.5 Other natural or manmade factors affecting its continued existence This factor category encompasses two specific threats to the species identified at the time of listing. These are: 1) environmental variability, including projected long-term climate change, and 2) stocking programs. Recent information about environmental variability, including the effects of ocean conditions on the survival of salmonid populations and increases in wildfire occurrence and severity, indicate that the threat from “environmental variability” can be expected to increase. Also, while stocking of non-native hatchery reared O. mykiss in anadromous waters has ceased, and triploid fish are used in current stocking programs, the legacy effects of past stocking of non-native hatchery reared O. mykiss has not been fully investigated in South-Central California Coast Steelhead DPS. 39 2.3.2.5.1 Environmental Variability
Variability in natural environmental conditions has both masked and exacerbated the problems associated with degraded and altered riverine, estuarine, and marine habitats. Floods and persistent drought conditions have periodically reduced naturally limited spawning, rearing, and migration habitats. Furthermore, El Niño events and periods of unfavorable ocean-climate conditions have resulted in significant swings in returning spawning run-sizes, and can threaten the survival of steelhead populations already reduced to low abundance levels due to the loss and degradation of freshwater and estuarine habitats. However, periods of favorable ocean productivity and high marine survival can temporarily offset poor habitat conditions elsewhere and result in dramatic increases in population abundance and productivity by increasing the size and correlated fecundity of returning adults.

Overall, the pattern of these threats have remained essentially unchanged since the last status review (Williams et al. 2011), though the threats posed by environmental variability (from projected climate change and related ocean conditions) are likely to exacerbate this factor affecting the continued existence of the species. See the discussion below (prepared by Crozier and Mantua in Williams et al. 2016).

2.3.2.5.2 Climate Effects
Projected impacts of future climate change on West Coast salmon Climatic conditions affect salmonid abundance, productivity, spatial structure, and diversity through direct and indirect impacts at all life-stages (e.g., Moyle et al. 2013, Wainwright and Weitkamp 2013, Crozier et al. 2008, Independenet Scientfic Advisory Board 2007, Lindley et al. 2007). Salmonids have adapted to a wide variety of climatic conditions in the past, and thus inherently could likely survive substantial climate change at the species level in the absence of other anthropogenic stressors.

Currently, the adaptive ability of these threatened and endangered species is depressed due to reductions in population size, habitat quantity and diversity, and loss of behavioral and genetic variation. Without these natural sources of resilience, systematic changes in local and regional climatic conditions due to anthropogenic global climate change will likely reduce long-term viability and sustainability of populations in many ESUs/DPSs. Adapting to climate change may eventually involve changes in multiple life-history traits and/or local distribution, and some populations or life-history variants might die out. Importantly, the character and magnitude of these effects will vary within and among ESUs/DPSs. See Figure 12. 40 ,,~ i.i \ ~ v"~- .,.
%:-~ · '.l':) 1,----- "" Stream Temp I --+---"--
I stream Flow 1-----1--"'
Returning
Spawners
Ocean
Residence
Smolts
I Stream Temp I
Upwelling; Sea
Temperat ure·
Current Streng, h
It
Figure 12. Conceptual model of factors affecting life-stages of Salmon and Steelhead.

The Intergovernmental Panel on Climate Change (IPCC) and U.S. Global Change Research Program recently published updated assessments of anthropogenic influence on climate, as well as projections of climate change over the next century (Melillo et al. 2014, Intergovernmental Panel on Climate Change 2013). Reports from both groups document ever-increasing evidence that recent warming bears the signature of rising concentrations of greenhouse gas emissions.

The U.S. Global Change Research Program report contains regional-focus chapters for the northwest (Mote et al. 2014, Snover et al. 2013) and southwest U.S. (Garfin et al. 2014). These regional reports synthesize information from an extensive literature review, including a broad array of analyses of regional observations and climate change projections. These synthesis reports were the primary source for this West Coast summary.

References to the primary literature can be found in those reports. Updates to this summary can be found in annual literature reviews conducted by NOAA-Fisheries (http://www.nwfsc.noaa.gov/trt/lcm/freshwater_habitat.cfm).

Historical Climate Trends
Observed historical trends in climate reflect the early influence of greenhouse-gas emissions, and often indicate the general direction of future climate change. These observations also reflect 41 natural variability in climate at multiple time scales. Natural variability alternately intensifies and relaxes (or partially reverses) the long-term trends. Attribution of historical trends to anthropogenic factors is most certain at the global scale over time scales of centuries to millennia because at these scales we can better account for natural variability.

Historical records show pronounced warming in both sea-surface and land-based air temperatures. There is moderate certainty that the 30-year average temperature in the Northern Hemisphere is now higher than it has been over the past 1,400 years. In addition, there is high certainty that ocean acidity has increased with a drop in pH of 0.1. Furthermore, glaciers and sea-ice have receded, while sea level has risen (global mean rose 0.19 m over the last century).

In recent decades, the frequency of extreme high temperature or heavy precipitation events has increased in many regions. An anthropogenic influence on this shift in frequency is “very likely” (Intergovernmental Panel on Climate Change 2014).

Regional and local trends include the following observations:
 In both the Northwest and Southwest:





air temperatures have increased since the late 1800s,
springtime snow-water equivalent has decreased (since 1950), snowmelt occurs earlier in the year.

In the Southwest, drought over the past 4 years is unprecedented in the historical record and may be the worst in over 1,000 years. This drought has been attributed to a combination of anthropogenic influence on temperature and natural variability in precipitation (Williams et al. 2015). Trends in precipitation vary spatially up or down, with no statistically significant trends in precipitation averages or extremes in the Northwest.

In both the Northwest and Southwest, widespread tree mortality has been observed, wildfires have increased in both frequency and area burned, and insect outbreaks have increased (Garfin et al. 2014. Mote et al. 2014).


Historical trends in the California Current are heavily influenced by patterns in wind-driven ocean circulation, which correlates with large-scale climate drivers such as the North Pacific Gyre Oscillation (Peterson et al. 2013) and Pacific Decadal Oscillation (Jacox et al. 2014). Spatially variable trends in upwelling intensity (Jacox et al. 2014) and hypoxia (Peterson et al. 2013), and longer trends in atmospheric forcing and sea surface temperature (Johnstone and Mantua 2014) probably reflect natural climate variability to a much greater extent than anthropogenic forcing.

The pH of the California Current has decreased by about 0.1 and by 0.5 in aragonite saturation state since pre-industrial times (Hauri et al. 2009). Furthermore, infrastructure in coastal areas is increasingly damaged by erosion and flooding (Garfin et al. 2014; Mote et al. 2014, Sweet et al. 2014).

Projected Climate Changes
General trends in warming and ocean acidification are highly likely to continue during the next century (Intergovernmental Panel on Climate Change 2103). Scenarios considered in the IPCC 42 fifth assessment report range from the severely curtailed greenhouse gas emissions of representative concentration pathway (RCP) 2.6 to business as usual in RCP 8.5.

Based on means across global climate models spanning the full breadth of these emissions scenarios, IPCC projected the following ranges across the Northern Hemisphere by 2081-2100:
 Spring snow cover declines of 7-25%
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

.

Glacier recessions of 15-85%
Sea surface temperature increases of 1.1-3.6°C
Global sea level increases of 11-38 inches
Global ocean pH decreases of 38 to 109%, which correspond to a drop in pH of

0.14-0.32
Regional projections add spatial variability and specificity to these projections. In winter across the west, the highest elevations (e.g. in the Rocky Mountains) will shift from consistently longer (>5 months) snow-dominated winters to shorter periods (3-4 months) of reliable snowfall (Klos et al. 2014); lower, more coastal or more southerly watersheds will shift from consistent snowfall over winter to alternating periods of snow and rain (“transitional”); lower elevations or warmer watersheds will lose snowfall completely, and rain-dominated watersheds will experience more intense precipitation events and possible shifts in the timing of the most intense rainfall (e.g., Salathe et al. 2014).

By the 2080s, Tohver et al. (2014) anticipate a complete loss of snow-dominated basins in the Cascades and U.S. portion of the Rockies, with only a few “mixed” basins of rain and snow-fed runoff remaining at the highest elevations. Flooding is projected to increase in basins that experience a mix of snow and rain in winter (Mote et al. 2014, Salathe et al. 2014, Tohver et al. 2014). Erosion and flooding in coastal areas are projected to increase with rising sea levels (Garfin et al. 2014, Mote et al. 2014, Sweet et al. 2014).

Among seasons, the greatest temperature shifts are expected in summer. Warmer summer air temperatures will increase both evaporation and direct radiative heating. When combined with reduced winter water storage, warmer summer air temperatures will lead to lower minimum flows in many watersheds. Higher summer air temperatures will depress minimum flows and raise maximum stream temperatures even if annual precipitation levels do not change (e.g., Sawaske and Freyberg 2014). Summer precipitation also influences summer flows, but projections for precipitation are less certain than for temperature. Coastal weather can differ from region-wide projections due to changes in fog, on-shore winds, or precipitation (Potter 2014, Johnstone and Dawson 2010).

Widespread ecosystem shifts are likely, and may be abrupt due to disturbances from increasing wildfires, insect outbreaks, droughts, and tree diseases (Garfin et al. 2014, Mote et al. 2014).

Climate projections often favor invasive fish species over native species, with declines exacerbated by the greater vulnerability of native species to existing anthropogenic stressors (Lawrence et al. 2014, 2012, Quiñones and Moyle 2014).

In response to projected changes in both climate and land use practices, estuary dynamics are expected to change as well, with depth and salinity altered by changing sea level, upwelling regimes, and freshwater input (Yang et al. 2015). Intense upwelling events can move hypoxic and acidic water into estuaries, especially when freshwater input is reduced (e.g., Columbia 43 River estuary, Roegner et al. 2011). Sea level projections differ at local vs. global scales due to local wind and temperature trends and land movement. Specifically, the National Research Council (2012) predicted a lower rise in sea level off the coasts of Washington and Oregon (62 cm) than off the coast of California (92 cm) by 2100.

Higher sea-surface temperatures and increased ocean acidity are predicted for marine environments in general (Intergovernmental Panel on Climatea Change 2013). However, regional marine impacts will vary, especially in relation to productivity. The California Current is strongly influenced by seasonal upwelling of cool, deep, water that is high in nutrients and low in dissolved oxygen and pH.

Ecological effects of climate change in the California Current are very sensitive to impacts on upwelling intensity, timing, and duration. Projections of how climate change will affect upwelling are highly variable across models, with predicted trends ranging from negative to positive (Bakun et al. 2010, Diffenbaugh et al. 2008, Snyder et al. 2003, Mote and Mantua 2002, Bakun 1990). An analysis of 21 global climate models found that most predicted a slight decrease in upwelling in the California Current, although there is a latitudinal cline in the strength of this effect, with less impact toward the north (Rykaczewski et al. 2015).

Much of the near-shore California Current is expected to be corrosive (undersaturated in aragonite) in the top 60 m during all summer months within the next 30 years, and year-round within 60 years (Gruber et al. 2012). Thermal stratification and hypoxia are expected to increase (Doney et al. 2014).

Impacts on Salmon and Steelhead
Studies examining the effects of long-term climate change to salmon and steelhead populations have identified a number of common mechanisms by which climate variation is likely to influence sustainability of salmon and steelhead populations. These include direct effects of temperature such as mortality from heat stress, changes in growth and development rates, and disease resistance. Changes in the flow regime (especially flooding and low flow events) also affect survival and behavior. Expected behavioral responses include shifts in seasonal timing of important life-history events, such as adult migration, spawning, fry emergence, and juvenile migration. The movement of juvenile steelhead between upstream stream reaches and the estuary may be disrupted by changes in late spring, summer and early fall base flows (e.g., Hayes et al. 2011, Boughton et al. 2009).

Indirect effects on salmon and steelhead mortality, growth rates and movement behavior are also expected to follow from changes in the freshwater habitat structure and the invertebrate and vertebrate community, which governs food supply and predation risk (Crozier et al. 2008, Independent Science Advisory Board 2007, Petersen and Kitchell 2001). Both direct and indirect effects of climate change will vary among Pacific salmon ESUs/DPSs and among populations in the same ESU/DPS. Adaptive change in any salmonid population will depend on the local consequences of climate change as well as ESU/DPS-specific characteristics and existing local habitat characteristics.

Because climate has such profound effects on survival and fecundity, salmon and steelhead physiology and behavior are intricately adapted to local environmental conditions. These adaptations vary systematically among populations and are exhibited in traits such as age and 44 timing of juvenile and adult migrations, with potential differences in physiology and migration routes (Quinn 2005). These traits often have a significant plastic (non-genetic) component, which allows them to respond quickly to environmental change. Yet these traits also differ genetically among populations (Carlson and Seamons 2008).

Directional climate change could, therefore, drive many salmonid populations into a maladaptive state. Such an outcome would likely cause reductions in abundance, productivity, population spatial structure and population diversity. In some cases, this can lead to extirpation if a population cannot adapt quickly enough. In other cases an adaptive solution may not exist because of conflicting pressures within or between life-stages.

Climate impacts in one life-stage generally affect body size or timing in the next life-stage. For this reason, the cumulative life-cycle effects of climate change must be considered to fully appreciate the scope of risk to a given population. Even without interactions among life-stages, the sum of impacts in many stages will have cumulative effects on population dynamics. See Figure 5.

Climate effects tend to be negative across multiple life-stages (Wade et al. 2013, Wainwright and Weitkamp 2013, Healey 2011). However, there may be mitigating responses in some ESUs/DPSs or life-stages. Individualistic impacts within and among ESUs/DPSs will depend on factors such as existing physical and biological heterogeneity, proximity to the limits of physiological tolerance under present climate conditions, and the extent of local climate change.

In many cases, directional climate change exacerbates existing anthropogenic threats. Examples include streams or rivers where stream temperatures are already elevated due to land-use modifications (Battin et al. 2007) or where flow is reduced due to water diversions (Walters et al. 2013). For example, in the Columbia River, dams have altered the hydrological regime by causing an earlier and smaller freshet, which is the same type of effect expected from climate change (Naik and Jay 2011a, Naik and Jay 2011b). Any of these stressors in combination with one another or with climate impacts will present pressures of much greater concern than they would individually, but they also offer potential solutions.

Changes in winter precipitation will likely affect incubation and/or rearing stages of most populations. Changes in the intensity of cool-season precipitation could influence migration cues for fall and spring adult migrants, such as coho and steelhead. Egg survival rates may suffer from more intense flooding that scours or buries redds.

Changes in hydrological regime, such as a shift from mostly snow to more rain, could drive changes in life-history, potentially threatening diversity within an ESU/DPS. It is possible that even characteristic life-history traits used to help define the ESU/DPS will be threatened. For example, the juvenile freshwater rearing period is very sensitive to temperature, with the yearling life-history strategy used only by populations in cooler watersheds (Beechie et al. 2006), or watershed with cooler refugia habitat. Frequency of the yearling life-history type will likely decline as movement downstream into estuaries or near-shore habitat is initiated at younger ages.

Implications of this behavioral shift for juvenile survival, ocean migration behavior, and age at maturity are uncertain.

Changes in summer temperature and flow will affect both juvenile and adult stages in some populations, especially those with yearling life-histories and summer migration patterns. 45 Juvenile rearing and migration survival is often correlated with these factors (Crozier et al. 2010, Crozier and Zabel 2006, Quinn 2005).

Adults that migrate or hold during peak summer temperatures can experience high mortality in unusually warm years. For example, in 2015 only 4% of adult Redfish Lake sockeye survived the migration from Bonneville to Lower Granite Dam after confronting temperatures over 22°C in the lower Columbia River. After prolonged exposure to temperatures over 20°C, salmon are especially likely to succumb to diseases that they might otherwise have survived (Miller et al. 2014, Materna 2001). They are also more vulnerable to any sort of stress, such as catch-andrelease fisheries (Boyd et al. 2010).

Changing hydrology and temperature will also affect the timing of smolt migrations and spawning (Crozier and Hutchings 2014, Hayes et al. 2014, Otero et al. 2014). If smolts migrate at a smaller size because they leave freshwater habitat earlier, they might have lower survival due to size-selective predation (Thompson and Beauchamp 2014, Hayes et al. 2008, Bond 2006).

Marine arrival timing is extremely important for smolt-to-adult survival (Scheuerell et al. 2009), and has been historically synchronized with the timing and predictability of favorable ocean conditions (Spence and Hall 2010). Given the uncertain effects of climate change on upwelling timing and intensity, impacts on juvenile survival from shifts in migration timing are also difficult to predict.

In some populations, behavior during the early ocean stage is consistent among years, suggesting a genetic rather than a plastic response to environmental conditions (Hassrick et al. In press, Burke et al. 2014). These populations might change their behavior over time if the fitness landscape changes, but responses will likely be relatively slow and could be dominated by decadal ocean dynamics or productivity outside the California Current (e.g., the Gulf of Alaska for northern migrants).

Other populations show more variable behavior after ocean entry (Fisher et al. 2014, Weitkamp 2010), and some show heightened sensitivity to interannual climate variation, such as the El Niño Southern Oscillation. Such variability might increase ESU/DPS-level resilience to climate change, assuming some habitats remain highly productive.

Marine migration patterns could also be affected by climate-induced contraction of thermally suitable habitat. Abdul-Aziz et al. (2011) modeled changes in summer thermal ranges in the open ocean for Pacific salmon and steelhead under multiple IPCC warming scenarios. For chum, pink, coho, sockeye and steelhead, they predicted contractions in suitable marine habitat of 30-50% by the 2080s, with an even larger contraction (86-88%) for Chinook salmon under the medium and high emissions scenarios (A1B and A2).

Northward range shifts are a climate response expected in many marine species, including salmon (Cheung et al. 2015). However, salmon and steelhead populations are strongly differentiated in the northward extent of their ocean migration, and hence will likely respond individualistically to widespread changes in sea surface temperature.

In most Pacific salmon species, size at maturation has declined over the past several decades.

This trend has been attributed in part to rising sea surface temperatures (Morita et al. 2005, Pyper and Peterman 1999, Bigler et al. 1996). Mechanisms involved in such responses are likely complex, but appear to reflect a combination of density-dependent processes, including increased competition due to higher salmon abundance in recent years and temperature (Pyper and 46 Peterman 1999). Temperature-related size effects could involve increased metabolic costs at higher temperatures, and/or shifts in spatial distribution in response to ocean conditions. Younger spawners affect population growth rates by exhibiting lower fecundity and reducing the population stability that stems from having multiple age classes reproduce.

Numerous researchers have reported that salmon and steelhead marine survival is highly variable over time and often correlated with large-scale climate indices (Litzow et al. 2014, Stachura et al. 2014, Sydeman et al. 2014, Petrosky and Schaller 2010, Mueter et al. 2005, 2002). For example, Pacific salmon from Washington and Oregon exhibited extremely low marine survival and dramatic population declines during a positive warm (positive) phase of the Pacific Decadal Oscillation in the 1980s and 1990s (Zabel et al. 2006, Levin 2003). These declines were attributed to low ocean productivity in the warm ocean of that period.

Many fish communities, including key salmon and steelhead prey and predators, experience changes in abundance and distribution during warm ocean periods (Cheung et al. 2009, Wing 2006, Pearcy 2002). However, food chain dynamics in the open ocean are flexible and difficult to predict into the future, and in the case of steelhead poorly understood (e.g., Grimes et al. 2007).

The full implications of ocean acidification on salmon are not known at this time (National Research Council 2010). Olfaction and predator-avoidance behavior are negatively affected in some fish species, including pink salmon (Ou et al. 2015, Leduc et al. 2013). Pink salmon also showed reductions in growth and metabolic capacity under elevated CO2 conditions (Ou et al. 2015). Some high-quality salmon prey (e.g., krill) might be negatively affected by ocean acidification, but there are several possible pathways by which higher trophic levels might compensate for changes at a lower trophic level. From their analysis of multi-trophic responses to ocean acidification, Busch et al. (2013) concluded that impacts to salmon could conceivably be positive. However, they emphasized that a better understanding of both direct and indirect feedback loops is necessary before drawing definitive conclusions.

To what extent a future warmer ocean will mimic historic conditions of warm-ocean, low-survival periods is not known. Current indications are that a warmer Pacific Ocean is generally less productive at mid latitudes, and hence likely to be less favorable for salmon and steelhead.

Analysis of ESU/DPS-specific vulnerabilities to climate change by life-stage will be available in the near future, upon completion of the West Coast Salmon Climate Vulnerability Assessment.

Climate effects on one Pacific salmon ESU, the Oregon coastal coho, were recently assessed by Wainwright and Weitkamp (2013). Below we present a summary of effects they reported for this ESU; many of these effects will likely be shared by other ESUs/DPSs, including the SouthCentral California Coast Steelhead Recovery Planning Area.

In summary, both freshwater and marine productivity tend to be lower in warmer years for most populations considered in this status review. These trends suggest that many populations might decline as mean temperature rises. However, the historically high abundance of many southern populations is reason for optimism and warrants considerable effort to restore the natural climate resilience of these species.
47 2012-2015 Drought Impacts on West Coast Salmon and Steelhead Habitat California has experienced well below average precipitation in each of the past 4 water years (2012-2015), record high surface air temperatures the past 2 water years (2014 and 2015), and record low snowpack in 2015. Some paleoclimate reconstructions suggest that the current 4-year drought is the most extreme in the past 500 or perhaps more than 1000 years. Anomalously high surface temperatures have made this a “hot drought”, in which high surface temperatures substantially amplified annual water deficits during the period of below average precipitation.

The combination of low precipitation and high temperatures has promoted elevated stream temperatures. The below normal precipitation and reduced runoff has adversely affected aquatic habitat for steelhead in a variety of other ways, resulting in: 1) depleted groundwater basins which provide base flows that support critical over-summering habitat for rearing O. mykiss; 2) reduced hydrological connectivity between seasonally wet and dry stream sections in interrupted streams; 3) restricted instream movement of rearing O. mykiss; 4) delayed or reduced breaching time of sandbars at the mouth of coastal estuaries, affecting water quality, and limiting both the upstream migration of adult O. mykiss and the downstream emigration of juveniles and kelts.

Riparian habitat has also been adversely affected by the reduction in groundwater levels and the reduction of surface flows, affecting water temperatures and food availability. 2014-15 Exceptionally Warm Ocean Conditions in the Northeast Pacific Much of the northeast Pacific Ocean, including parts typically used by California salmon and steelhead, experienced exceptionally high upper ocean temperatures beginning early in 2014 and areas of extremely high ocean temperatures continue to cover most of the northeast Pacific Ocean. A plume of warm water formed offshore of the Pacific Northwest region in fall 2013 (Bond et al. 2015). Off the coast of Southern and Baja California, upper ocean temperatures became anomalously warm in spring 2014, and this warming spread to the Central California coast in July 2014. In fall 2014, a shift in wind and ocean current patterns caused the entire northeast Pacific domain to experience unusually warm upper ocean temperatures from the West Coast offshore for several hundred kms. In spring 2015 nearshore waters from Vancouver Island south to San Francisco mostly experienced strong and at time above average coastal upwelling that created a relatively narrow band (~50 to 100 km wide) of near normal upper ocean temperatures, while the exceptionally high temperature waters remained offshore and in coastal regions to the south and north.

Expectations for Future Climate Risks and Impacts Already in the Pipeline for West Coast Salmon and Steelhead
As with most upstream migrations of anadromous salmonids along the California coast, adult coho salmon returns this fall/winter and in the fall 2016/winter 2017 have likely been negatively impacted by poor stream and ocean conditions. Adult salmon and steelhead returns for this fall (next winter) and for the next 2 to 3 years (depending on ocean residence times, maturing in 2015-2018) have likely been negatively impacted by poor stream and ocean conditions.

The expected effects of the 2015/16 tropical El Niño are likely to favor a more coastally-oriented warming of the Northeast Pacific this fall and winter that will persist into spring 2016. Next spring’s ocean migrants will likely encounter an ocean strongly influenced by (if not dominated 48 by) a subtropical food-web that favors poor ocean survival (Nate Mantua, NOAA Southwest Fisheries Science Center, Santa Cruz Laboratory, personal communication 2015).

Summary
Four consecutive years of drought and the past two years of exceptionally high air, stream and upper-ocean temperatures have together likely had negative impacts on the freshwater, estuary, and marine phases for many populations of salmon and steelhead. In addition to reducing over summering and migration flows, in the South-Central California Coast Steelhead DPS, the drought has also resulted in a number of rivers and streams remaining closed at their mouths as a result of insufficient flows to breach the sandbar at the river mouth, or reducing the times the river mouths are open to the ocean (Rich and Keller 2011, Jacobs et al. 2010). Delayed or prolonged river mouth has limited the upstream migration of adults and the downstream emigration of juveniles (smolt) or adults (kelts); low flows may have also interrupted the natural periodic movement of sub-adults between the estuary and the ocean which has been documented in some systems in the North Central California Coast Steelhead DPS.

NOAA’s Climate Prediction Center (CPC) forecasts a 95% likelihood that the tropical El Niño event will persist through the winter of 2016, and they also predict a high likelihood for this event to alter North Pacific and Western US climate for the next few seasons. Seasonal climate forecasts issued by CPC in mid-September show increased odds for typical El Niño fall/winter climate conditions that include above average fall and winter temperatures in West Coast states, increased odds for below normal precipitation in the Pacific Northwest (especially large increases in the odds for a dry fall/winter in the interior Columbia Basin), and increased odds for a wet fall in Southern California, and a wet winter in all of California. Because El Niño events favor fall/winter periods with an especially strong Aleutian Low pressure anomaly centered in the Gulf of Alaska, the exceptionally warm upper ocean temperatures off the Pacific Northwest coast is expected to weaken considerably. In contrast exceptionally warm ocean temperatures between Central, Southern, and Baja California and Hawaii are expected to remain elevated for the next few seasons. El Niño-related changes in wind and related ocean current patterns are expected to cause a coast-wide warming of upper ocean temperatures from Alaska south to Mexico, but confined to a relatively narrow band within ~ 100 miles of the coast.

In summary, the strong El Niño event is predicted to substantially reduce the odds for a repeat of the extreme warmth of the past 2 winters, the extreme precipitation deficit experienced throughout California the past 4 winters, and the extreme warmth of the offshore waters of the Northeast Pacific Ocean that have persisted for most of the past 2 years. The past 2 years have also seen persistence in the warm phase PDO pattern of North Pacific Ocean temperatures, and the warm phase of the PDO is likely to continue for another year because of it strong tendency for persistence and the expected El Niño influences on the Aleutian Low and related ocean currents in the next 6 months.

2.3.2.5.3 Stocking Program
There is no steelhead production hatchery operating in or supplying hatchery reared steelhead for stocking into streams within the range of the South-Central California Coast Steelhead DPS.

However, there is a CDFW stocking program of hatchery cultured and reared, non-anadromous O. mykiss which supports a “put-and-take” fishery that is stocked for removal by anglers. These 49 stockings are now conducted in non-anadromous waters (using triploid fish). However, other non-native game species such as large and smallmouth bass and bullhead catfish are stocked into anadromous waters by a variety of public and private entities).

While some of these stocking programs have succeeded in providing seasonal fishing opportunities, the impacts of these programs on native, naturally-reproducing steelhead stocks are not well understood. Competition, genetic introgression, and disease transmission resulting from hatchery introductions may significantly reduce the production and survival of native, naturally-reproducing steelhead (Araki et al. 2009, 2008, 2007). However, genetic investigations of southern California steelhead have detected limited interbreeding and displacement of native steelhead with hatchery reared O. mykiss, particularly in the southernmost portions of the SouthCentral/Southern California Steelhead Recovery Planning Domain DPS (Adadia-Cardoso, et al. 2016, Jacobson et al. 2014, Abadia-Cardoso et al. 2011, Christie et al. 2011). As noted, these stockings are now carried out in non-anadromous waters, though fish in some cases may escape into anadromous waters. Collection of native steelhead for hatchery broodstock purposes can harm small or dwindling natural populations. Artificial propagation can also, in some situations, play an important role in steelhead recovery through, among other means, preservation of individuals representing genetic resources which would otherwise be lost as a result of local anthropogenic driven extinctions, but are not a substitute for naturally-reproducing populations.

Overall, threats from stocking have remained essentially unchanged since the last status review (Abadia-Cardoso et al. 2016, Williams et al. 2016, Williams et al. 2011). Thought the extent of legacy effects of past stocking is now better understood in some areas.

2.4 Synthesis

2.4.1 DPS Status
There is little new evidence to indicate that the status of the South-Central California Coast Steelhead DPS has changed appreciably in either direction since the last status review (Williams et al. 2011), though as noted above, the Carmel River runs have shown a long term decline, likely exacerbated by the extended drought, and possible the reliance on hatchery reared juvenile O. mykiss. The extended drought and the lack of comprehensive monitoring, has also limited the ability to fully assess the status of individual populations and the DPS as whole.

The systemic anthropogenic threats identified at the time of the initial listing have remained essentially unchanged over the past 5 years, though there has been significant progress in removing fish passage barriers in a number of the smaller and mid-sized watersheds. Threats to the South-Central California Coast DPS posed by environmental variability resulting from projected climate change are likely to exacerbate the factors affecting the continued existence of the DPS.

2.4.1 Recovery Progress
While the status of the populations of steelhead within the South-Central California Coast Steelhead DPS has not changed appreciably since the last status review, a number of recovery 50 related activities have been undertaken which may result in some reduction in threats to the species, and potentially lead to a future increase in individual populations as other habitat conditions (including resumption of winter flows) improve.

The removal of San Clemente Dam and construction of step pools through the new channel removed a major impediment to fish migration and also will contribute to the re-establishment of a more natural hydrologic and sediment regime in the lower Carmel River; additionally feasibility studies have been initiated on the potential removal of the upstream Los Padres Dam which would open up volitional access to additional upstream spawning, and rearing habitat within the Carmel River watershed. In the interim, fish passage has been provided for the passage of upstream migrating adults, and downstream emigrating smolts and kelts at Los Padres Dam.

Water releases from Uvas Dam have been provided to improve downstream habitat for steelhead in Uvas Creek, a major spawning and rearing tributary within the Pajaro River watershed. The modification of the water releases from the Pacheco Dam on Pacheco Creek (a tributary to the Pajaro River) has provided improved flow conditions for steelhead during critical periods.

A number of recovery actions have been undertaken on the Salinas River, the largest river system within the South-Central California Coast Steelhead Recovery Planning Area. These include implementation of the Salinas River Multi-Demonstration Project by The Nature Conservancy to provide more environmentally sound flood control and vegetation management.

A number of restoration projects have focused on the removal of non-native invasive species (e.g., Sacramento Pikeminnow in Chorro Creek, Arundo removal in San Luis Obispo Creek, Eucalyptus in Santa Rosa Creek), riparian/bank restoration of Corral de Piedra in Pismo Creek, riparian fencing in Coon Creek, and riparian restoration in Walters Creek, tributary to Morro Bay). Rainwater harvesting during winter months has been undertaken at Cal Poly San Luis Obispo to reduce extraction of summer flows in Pennington Creek, tributary to the Morro Bay Estuary. And storm water management programs have been instituted in the Morro Bay watershed.

Funding for these projects was provided by the California Coastal Conservancy, CaliforniaAmerican Water Company, California Wildlife Conservation Board, Pacific Coastal Salmon Recovery Fund (PCSRF), the CDFW Fisheries Restoration Grant Program (FRGP), National Fish and Wildlife Foundation, and the NOAA Restoration Center, and the American Recovery and Reinvestment Act. Additionally, local entities, including jurisdictions (e.g., City of San Luis Obispo, City of Watsonville, County of Santa Cruz, Monterey County Water Agency, Monterey Peninsula Water Management District, Morro Bay National Marine Estuary Program, San Luis Resource Conservation District, and Upper Salinas-Las Tablas Resource Conservation District) and Non-Governmental Organizations (e.g., AmeriCorps and National Civilian Community Corps, California Conservation Corps – Los Padres Service District, Carmel River Steelhead Association, Central Coast Salmon Enhancement, Coastal Habitat, Education, and Environmental Restoration [CHEERS], Garrapata Creek Watershed Committee, Land Conservancy of San Luis Obispo County, Los Padres Forest Watch, Monterey Bay Trout Project, Tri-Counties Fish Team, CalTrout, Trout Unlimited, Upper Salinas Watershed Coalition, and the 51 Ventana Wilderness Alliance), have contributed substantial organizational, in-kind services, and financial support for the implementation of recovery projects.

The CDFW has expanded its use of sterile (triploid) fish to include all the watersheds currently stocked with O. mykiss to prevent the interbreeding of hatchery-reared fish with native steelhead.

NMFS also issued a Biological Opinion to NOAA’s Restoration Center to cover restoration projects funded by the Restoration Center, or projects that require a section 404 permit from the U.S. Army Corps Engineers that are determined by the Restoration Center to be within the scope of the program. To specifically qualify, all proposed restoration projects must satisfy one or more of the following objectives: 1) restore degraded steelhead habitat, 2) improve instream cover, pool availability, and spawning gravel; 3) remove barriers to fish passage; and 4) reduce or eliminate sources of erosion and sedimentation. Due to the evolving nature of the various techniques and guidelines for salmonid restoration, the NOAA’s Restoration Center requires that projects authorized under this program must adhere to the most current practices and best available guidelines and techniques for design and implementation. NMS also issued a Biological Opinion to the U.S. Army Corps of Engineers and the Natural Resources Conservation Service for conservation practices conducted under the Upper Pajaro River Watershed Partners in Restoration Permit Coordination Program in San Benito and Santa Clara counties.

NMFS has also conducted both formal and informal Section 7 Consultations with federal agencies throughout the DPS that fund, carry out, or regulate projects such as flood protection, road construction, water diversion, bridge replacements, and gravel mining operations.

3.0 RESULTS

3.1 Recommended Classification and DPS Boundary
Based upon a review of the best available information, we recommend that the South-Central California Coast steelhead DPS remain classified as a threatened species. Similarly, we do not recommend any changes to the geographic boundary of this DPS at this time. NOAA’s Southwest Fisheries Science Center, Santa Cruz Laboratory, convened a Biological Review Team to evaluate all new genetic information for this and the other coastal steelhead DPSs in California but has not completed its review. The Southwest Fisheries Science Center will provide the West Coast Region with an analysis of this and other information which will be subsequently evaluated by the Region to determine whether any changes in the DPS boundary is warranted.

3.2 New Recovery Priority Number
No change is recommended in the recovery priority number 3 for this DPS.

4.0 RECOMMENDATIONS FOR FUTURE ACTIONS
The following recommendations are based on the 2015 status review and are intended to focus recovery activities within the South-Central California Coast Steelhead Recovery Planning 52 Domain in a manner that implements the provisions of the South-Central California Steelhead Recovery Plan. These activities focus on five major areas: 1) monitoring, 2) research, 3) regulation, 4) recovery actions, and 5) the prevention of local extirpations of steelhead populations.

4.1 Monitoring
The status review confirms the value and need for the California CMP. Full implementation of the California CMP is necessary to accurately understand the risk to the South-Central California Coast Steelhead DPS, and assess the response of the DPS to the various recovery actions that have been undertaken to date, or will be in the future. Additionally, information gathered through the California CMP is necessary to refine the viability criteria. To address these issues we recommend the following actions:
 Update and fully implement the California CMP abundance monitoring and spatialstructure monitoring (consistent with the changes discussed above; see Sections 2.3.1.4 through 2.3.1.4.1);



Add the monitoring of resident adults and genetic diversity to the California CMP (as discussed above; see Sections 2.3.1.4 through- 2.3.1.4.1); Greater emphasis be placed on monitoring methods that are unbiased or can be biascorrected (as discussed above); Site-selection and initiation of LCM stations as identified in the South-Central California Steelhead Recovery Plan as discussed above in Sections 2.3.1.4 through 2.3.1.4.1. See also Table 13-1, “Potential Locations of South-Central California Coast Steelhead LifeCycle Monitoring Stations” in the South-Central California Steelhead Recovery Plan.

Among other benefits, these LCM stations could serve as study sites to clarify the role of the putative chromosome inversion in the maintenance of life-history diversity, and to clarify the potential smolt production of the medium and large alluvial rivers, such as Salinas, Pajaro, Carmel, San Carpoforo, San Luis Obispo, Pismo, and Arroyo Grande; and
 Identification of drought refugia as provided in the South-Central California Steelhead Recovery Plan; current (and projected) future droughts provide a valuable opportunity to identify and characterize drought refugia.
53 4.2 Research
Initiate the research into steelhead ecology identified in the South-Central California Steelhead Recovery Plan and identified in the NCEAS Southern steelhead research and monitoring colloquium. Important research topics include:
 Ecological factors that promote anadromy;








Reliability of migration corridors;
Steelhead-promoting nursery habitats;
Comparative evaluation of seasonal lagoon/estuaries;
Potential nursery role of mainstem habitats;
Potential positive spawner density as an indicator of viability; Role of naturally intermittent river and stream reaches; Partial migration and life-history crossovers; and
Rates of dispersal between watersheds.

4.3 ESA Section 7 Consultations and Section 10 Permitting Activities.

Focus on completing and implementing key ESA Section 7 consultations and Section 10 permitting actions in core watersheds that address the most fundamental threats to the SouthCentral California Coast Steelhead DPS, i.e., though addressing fish-passage and flow issues.

These include:
 Interlake Tunnel Project, Salinas River (Monterey County Water Resources Agency);


Upper Llagas Creek Flood Control Project, Pajaro River (U.S. Army Corps of Engineers); and
Lopez Dam Habitat Conservation Plan, Arroyo Grande Creek (County of San Luis Obispo).

Issue Section 10 scientific research permits that support the research and monitoring activities identified above; see also Sections 2.3.1.4 through 2.3.1.4.1 .

4.4 High Priority Recovery Actions
Additionally, high priority recovery actions identified in the South-Central California Steelhead Recovery Plan should be implemented. These actions include:
 Identify and remove man-made steelhead-passage barriers in all core population watersheds:
54 • Re-establish access to upper watersheds in both small coastal streams (e.g., San Jose, Pismo and Arroyo Grande creeks) and the larger interior river systems (e.g., Salinas, Pajaro, and Carmel rivers) within each BPG identified by the TRT (See Table 5).
• Complete planning for the potential removal of Los Padres Dam on the Carmel River.



Provide ecological meaningful flows below dams and diversions in all core population watersheds:
• Re-establish adequate flow regimes in both small coastal stream (e.g., San Jose Creek, Santa Rosa Creek, Morro Bay tributaries, Arroyo Grande Creek) and the larger interior river systems (e.g., Pajaro River, Salinas River, Carmel River, Big Sur River).

Complete the Fisheries Management and Enhancement Plan (FMEP).

4.5. Preventing Local Extinctions of O. mykiss
The extended drought and drying conditions associated with projected climate change has the potential to cause local extinction of O. mykiss populations and thus reduce the genetic diversity of fish within the South-Central California Coast Steelhead Recovery Planning Area. To reduce this risk the following measures should be undertaken:
 Maintain the conservation hatchery functions of the CDFW Fresno hatchery, and where appropriate, expand its capability to accommodate the temporary accommodation of fish removed from the wild to prevent their extirpation; and Explore other means of conserving individual stocks of O. mykiss which may face the risk of extirpation (e.g., using other existing facilities at academic institutions or museums, or natural refugia habitats).
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72 NATIONAL MARINE FISHERIES SERVICE
5-YEAR REVIEW
South-Central/Southern California Coast Steelhead Recovery Domain South-Central California Coast Steelhead DPS
Current Classification: Threatened
Recommendation resulting from the 5-Year Review: Retain current ESA classification as threatened and current DPS boundary.

REGIONAL OFFICE APPROVAL:

Approve: --~.::.....;_ --~- ·<________ Date: 3/'J--'f/Jk, ~ I Alecia Van Atta
Assistant Regional Administrator
California Coastal Office
West Coast Region
National Marine Fisheries Service
73 906 Garden St. Santa Barbara, CA 93101
PHONE (805) 963-1622 FAX (805) 962-3152
www.EnvironmentalDefenseCenter.org
March 25, 2021
Alan B. Lilly, Presiding Hearing Officer
State Water Resources Control Board
P.O. Box 100
Sacramento, CA 95812-0100
Submitted via email to [email protected] Re: City of Solvang Petitions: California Trout Status Conference Statement Dear Mr. Lilly:

This response to the City of Solvang’s Status Conference Statement is submitted on behalf of California Trout (“CalTrout”). Pursuant to the Notice of New Status Conference Date, dated January 15, 2021, the City was required to submit a Statement describing: (1) the supplemental hydrological, environmental, and other analyses that Solvang plans to conduct for its amended change petition, (2) the new California Environmental Quality Act (“CEQA”) document that Solvang will prepare for its amended change petition, and (3) Solvang’s proposed schedule for completing these analyses and documents.

As explained herein, the City’s proposal to prepare an Addendum to the 2014 Master Plan Update Environmental Impact Report (“EIR”) (“2014 EIR”) is inappropriate under CEQA given changes in the circumstances under which the project will be carried out, and new information regarding significant impacts. In addition, the City’s reliance on the Stetson Engineers, Inc. Memoranda is misplaced and outdated, and the proposed study plan for GSI is deficient, because they pre-suppose the outcome of the required analyses and are based on outdated, irrelevant information.

The State Water Resources Control Board (“SWRCB”) should direct the City to prepare a subsequent EIR pursuant to CEQA Guidelines Section 15162. The SWRCB should further direct the City to conduct hydrological, environmental, and other analyses that are based on the current conditions and requirements for flows in the Santa Ynez River and updated information regarding the status of public trust resources in the River, including endangered Southern California steelhead.

March 25, 2021
CalTrout Response to City of Solvang March 12, 2021 Status Conference Statement