Adult spring-run return monitoring during 2016 …...ii Adult Spring-run Chinook Salmon return monitoring during 2016 within the San Joaquin River, California Prepared by: Judith Barkstedt

Adult Spring-run Chinook Salmon return

monitoring during 2016 within the San

Joaquin River, California

Annual Technical Report

ii

Adult Spring-run Chinook Salmon return

monitoring during 2016 within the San

Joaquin River, California

Prepared by:

Judith Barkstedt1, Crystal Castle

1, Garrett Giannetta

1, and Joseph Kirsch

12*

1 U.S. Fish and Wildlife Service, 850 S. Guild Ave, Suite 105, Lodi CA 95240

2Present address: USDA Forest Service, PO Box 545, Copperopolis, CA 95228

*Corresponding author: [email protected]

June 2017

iii

EXECUTIVE SUMMARY

The main stem San Joaquin River historically supported naturally self-sustaining populations of fall-run

and spring-run Chinook Salmon Oncorhynchus tshawytscha. The construction of Friant Dam and

subsequent water management practices led to the extirpation of salmon runs within the San Joaquin

River above the confluence with the Merced River. As a result of NRDC et al. v. Kirk Rodgers et al

lawsuit, a Stipulation of Settlement (Settlement) was reached that established a framework for

accomplishing the Restoration and Water Management goals that will require environmental review,

design, and construction of projects over a multiple-year period. The Settlement created the San Joaquin

River Restoration Program (Program) with the goal to restore and maintain fish populations in “good

condition” from Friant Dam to the confluence with the Merced River. To facilitate the reestablishment of

spring-run Chinook Salmon into the San Joaquin River, the Program implemented direct releases of

approximately 60,000 juvenile spring-run Chinook Salmon from Feather River hatchery stock into the

San Joaquin River beginning in 2014. The Program hypothesized that an estimated total of 21 (±4) adult

spring-run salmon would return to the Restoration Area as early as the spring of 2016 based on the

numbers of juveniles released and historical hatchery fish return data. We conducted real-time adult

spring-run salmon return monitoring during 2016 to determine the survival, distribution, and habitat use

of adult spring-run salmon returning to the restoration area that were released by the Program in 2014.

We passively monitored returning adult spring-run salmon using a Vaki Riverwatcher Fish Counter

paired with a V-shaped net weir from March through June at Hills Ferry located at the most downstream

section of the restoration area just above the confluence of the Merced River. The Vaki Riverwatcher Fish

Counter consisted of two infrared scanner plates and produced at least one silhouette image of each

passing fish with a body depth greater than or equal to 4 cm. The Vaki Riverwatcher Fish Counter and net

weir were checked 3–5 times each week throughout the sampling period to ensure stability and proper

function. If adult spring-run returns are detected, a fyke trap will be installed and checked daily to capture

individuals passing through the Vaki unit. Captured adult spring-run would be transported to Reach 1 of

the Restoration Area. More than 1,700 fish were scanned during the sampling period, but Chinook

Salmon were not detected. To ensure that salmon were not misidentified, we evaluated the identification

accuracy of our observers using Vaki Riverwatcher Fish Counter silhouettes of known fish species

collected in other rivers within the Central Valley. In addition, our identification of fish using silhouette

data was verified by other local Vaki Riverwatcher Fish Counter experts and users. In general, we

postulate that our lack of adult spring-run salmon detections may be the result of no returning adults

passed this location during the monitoring period? We recommend that the Program continue monitoring

returning adult spring-run salmon in subsequent years using our methods along with gear efficiency

calibration tests.

The preferred citation for this report is:

Barkstedt, J., C. Castle, G. Giannetta, and J. Kirsch. 2017. Adult Spring-run Chinook Salmon return

monitoring during 2016 within the San Joaquin River, California. Annual Technical Report. U.S. Fish and

Wildlife Service, Lodi, California.

iv

Disclaimer: Any use of trade, firm, or product names is for descriptive purposes only and does not imply

endorsement by the U.S. Government.

v

Table of Contents

1.0 Adult Spring-run Chinook Salmon return monitoring during 2016 within the San Joaquin River,

California ...................................................................................................................................................... 1

1.1 Introduction ......................................................................................................................................... 1

1.1.1 Objectives: .................................................................................................................................. 2

1.2 Methods.............................................................................................................................................. 2

1.2.1 Study Area .................................................................................................................................. 2

1.2.2 Sampling Design ......................................................................................................................... 3

1.2.3 River Conditions ......................................................................................................................... 5

1.2.4 Fish Identification ....................................................................................................................... 5

1.2.5 Calibration Testing ...................................................................................................................... 6

1.3 Results ................................................................................................................................................. 6

1.3.1 Adult Return Monitoring ............................................................................................................ 8

1.3.2 Calibration Testing ...................................................................................................................... 9

1.4 Discussion ........................................................................................................................................ 11

1.5 References ......................................................................................................................................... 14

Abbreviations and Acronyms

CDFW California Department of Fish and Wildlife

CWT Coded-wire tag

BY Brood year

TL Total length

NMFS National Marine Fisheries Service

NTU Nephelometric turbidity unit

RKM River kilometer

Program or SJRRP San Joaquin River Restoration Program

USFWS U.S. Fish and Wildlife Service

Vaki Vaki Riverwatcher Fish Counter

1

1.0 Adult Spring-run Chinook Salmon return

monitoring during 2016 within the San Joaquin

River, California

1.1 Introduction

The main stem San Joaquin River historically supported naturally self-sustaining populations of

fall-run and spring-run Chinook Salmon Oncorhynchus tshawytscha (Fry 1961; Fisher 1994).

The construction of Friant Dam in 1942 and subsequent water management practices led to

extensive habitat degradation and recurring river fragmentation (i.e., desiccated river reaches)

within the main stem San Joaquin River upstream of the confluence of the Merced River

(Yoshiyama et al. 2001; Williams 2006). These alterations have attributed to the extirpation of

all salmon runs within the San Joaquin River above the confluence of the Merced River

(Yoshiyama et al. 2001).

A settlement resulting from Natural Resource Defense Council, et al., v. Rodgers, et al. (2006)

created the San Joaquin River Restoration Program (Program). The goals of the Program are to

restore and maintain fish populations in “good condition” in the main stem San Joaquin River

downstream of Friant Dam to the confluence with the Merced River (Restoration Area) including

naturally reproducing and self-sustaining populations of salmon and other fish (Restoration

Goal) while reducing or avoiding adverse water supply impacts to all of the Friant Division long-

term contractors that may result from the Interim Flows and Restoration Flows provided for in

the Settlement (Water Management Goal; SJRRP 2010). To restore spring-run into the San

Joaquin River, the U.S. Fish and Wildlife Service (USFWS) was permitted by the National

Marine Fisheries Service (NMFS) under the authority of section 10(a)(l)(A) of the Endangered

Species Act of 1973 to conduct direct releases of juvenile spring-run salmon from Feather River

Fish Hatchery stock into the San Joaquin River each year from 2014 through 2019 (SJRRP 2012;

NMFS 2014; SJRRP 2015). The efficacy of implementing direct juvenile salmon releases from

donor stocks into the San Joaquin River is to restore the spring run population, anticipating that

some of those fish will complete their life-cycle and contribute to future generations (SJRRP

2011).

The Program released an estimated total of 60,114 and 54,839 juvenile spring-run Chinook

Salmon from the Feather River Fish Hatchery directly into the Restoration Area during the

spring of 2014 and 2015, respectively. All juveniles were adipose fin clipped and implanted with

a coded-wire tag (CWT) in their nasal cartilage that contained a batch number representing their

origin and release group. During each year, juveniles were transported from the Feather River

Fish Hatchery to the Restoration Area and held in net pens below Friant Dam for 3–5 days to

2

increase the likelihood of “imprinting” on San Joaquin River water. Thereafter, the juvenile fish

were transported to the most downstream stretch of the Restoration Area below all passage

impediments (e.g., desiccated reaches and structural barriers) and were released just upstream of

the confluence with the Merced River.

The Program’s Fisheries Management Work Group estimated that a total of 21 (± 4) adult

spring-run salmon representing age-3 adults from brood year (BY) 2013 and age-2 adults from

BY 2014 may return to the Restoration Area during the spring of 2016 between February and

June (Kirsch et al. 2016). This hypothesis was derived from the hatchery fish return estimates

presented in the Program's Revised Framework for Implementation (SJRRP 2015), which was

based on the numbers of juveniles released and historic hatchery fish return data. Unfortunately,

fish passage barriers currently prevent the volitional passage of returning adult spring-run salmon

to suitable holding and spawning habitat within the Restoration Area. As a result, management

actions (e.g., adult translocation) are needed to pursue salmon reestablishment, fulfill compliance

requirements, and facilitate the learning necessary to properly inform adaptive fishery

management decisions (SJRRP 2009; SJRRP 2010; Kirsch et al. 2016). Therefore, adult spring-

run salmon return monitoring was needed in 2016 to evaluate the performance of direct juvenile

releases (or test hypothesis of FMWG) and to inform management decisions including the need

to implement adult translocation actions.

1.1.1 Objectives:

To evaluate the performance of spring-run Chinook Salmon reintroduction actions and to inform

adaptive management decisions, we passively monitored returning adults in Reach 5 (Figure 1)

of the Restoration Area during the spring of 2016. We monitored adult spring-run salmon

returning to the Restoration Area with the following objectives:

1. Determine the abundance and temporal distribution of adult spring-run salmon returning

to Reach 5 of the Restoration Area.

2. Inform management decisions if salmon are detected, which may include initiating trap

and transport of adults around stream barriers to spawning grounds in Reach 1 (Figure 1).

3. Assess the efficiency of the Vaki gear used to passively monitor returning adult salmon.

1.2 Methods

1.2.1 Study Area

The San Joaquin River originates on the western slope of the Sierra Nevada, and flows westward

past Fresno, California onto the Central Valley floor and northward into the San Francisco

Estuary. The Restoration Area spans 246 river kilometers (RKM) and is divided into 5 reaches

(Figure 1). Currently, Reach 1 contains losing reaches that possess all suitable salmon spawning

3

habitat in the Restoration Area. In reaches 2–4, the river is dry or discharge is intermittent during

non-flood conditions with the exception of where irrigation water from the federal Central

Valley Project is being conveyed in the main river channel (e.g., Reach 3). The lower portion of

Reach 5 often conveys consistent flow generated by a combination of agricultural return water

coming from Mud and Salt sloughs, effluent from the Newman Wasteway, and seasonal

rainwater runoff. We monitored returning adult spring-run Chinook Salmon at Hills Ferry

located at the most downstream end of the Restoration Area, immediately upstream of the

confluence with the Merced River (Figure 1).

Figure 1. Map of the San Joaquin River with reach designations. The spring-run return

monitoring occurred in Reach 5 at Hills Ferry, the downstream-most reach of the San Joaquin

River Restoration Area.

1.2.2 Sampling Design

Returning adult spring-run Chinook Salmon were monitored continuously and passively by a

Vaki Riverwatcher Fish Counter unit (henceforth Vaki unit; Vaki Aquaculture Systems LTD,

Kópavogur, Iceland) from March 3 to June 8, 2016, which included the hypothesized period of

distribution of non-lethal temperatures. In general, Vaki units are used in conjunction with

4

permanent weirs or fish passage structures to count migrating adult Chinook Salmon and

steelhead O. mykiss within multiple rivers in the Central Valley including Butte Creek, Yuba

River, Stanislaus River, and Tuolumne River.

We mounted the Vaki unit to a tower anchored in the substrate that was constructed of

perforated, galvanized steel, 4.5-cm square tube posts. The tower was positioned in the thalwag

of the channel and suspended the Vaki unit underwater approximately 1 m above the riverbed.

The Vaki unit’s frame was connected to an opening in a 2-m tall net weir that consisted of two

wing walls with 4.45-cm square knotless nylon netting (8.9-cm stretch), small floats spaced

every 91 cm on top, and a 90.7-kg lead core line on bottom.

In general, the wing walls varied in length (48 m on river right and 29 m on river left) and

collectively spanned across the river channel while accommodating boat passage with a 5–10-m

long opening on river left (Figure 2). The net weir was held in place by 3.1-m tall t-posts spaced

every 1.5 m in net length. The net weir extended downstream towards each shoreline in a v-

shaped pattern with the net entrance facing downstream. The river-right wing extended to the

shoreline and the river-left wing was shortened to leave approximately 10 m for boat passage

when monitoring was first initiated. An additional 12.1-m wing-wall was added downstream of

the river-left wing on April 18, 2016 to increase net coverage across the river channel while still

allowing for boat passage (Figure 2). We marked the net weir, t-posts, and the tower using highly

visible flagging, night lights, and orange buoys to provide visual warning cues for boaters. In

addition, we also placed warning signs for boaters approximately 100-m downstream and

upstream of the gear.

5

Figure 2. Conceptual diagram of the Vaki unit and net weir used in the San Joaquin River at

Hills Ferry in Reach 5 near Newman, California. The additional 12.1-m wing-wall was added on

April 18, 2016 to increase coverage across the river channel.

The Vaki unit was configured to scan and record the silhouette of each fish that passed between

the scanner plates. The scanner plates within the Vaki unit were spaced 42.5 cm apart, but were

moved closer together (25.5 cm apart) when we hypothesized that diode visibility was reduced in

turbid conditions. The scanners were programmed to only record fish silhouettes more than 4 cm

in body depth to focus on adult Chinook Salmon and minimize data storage. Information

recorded for each fish of adequate body depth included two silhouette images, silhouette depth

(cm), pass direction (upstream, downstream), date, time, temperature, and diode functionality.

Length (cm) information is calculated from the body depth measurement using a generic length-

depth ratio of 6. This ratio can be altered based on the species identified; however, we used this

ratio for all silhouettes because it was the default setting.

All information collected by the scanner unit was stored in a control unit powered by a deep

cycle battery that was recharged using solar panels. The control unit and power supply was

housed in a waterproof box located in a heavy duty metal storage box secured to a concrete slab

on the riverbank. A 50–100 m communication cable connected the control unit and power supply

to the scanner unit, and was secured to the river bottom using perforated, galvanized steel, 4.5-

cm square tube posts. The Vaki unit and wing walls were checked 2–5 times each week

throughout the sampling period to ensure proper function and net stability. We repaired any

holes in the net that were detected and filled in gaps between the substrate and the lead core line

using sandbags. Data stored on the control unit was downloaded to an external hard drive or

laptop each day the equipment was checked. This data were subsequently stored and analyzed

using Winari software (VAKI©, ver. 4.43) located at the Lodi Fish and Wildlife Office.

1.2.3 River Conditions

To describe river conditions during the study period, we compiled and plotted continuously

recorded mean daily discharge (m3/s), turbidity (nephelometric turbidity units, NTU; Hach®

turbidimeter Model 2100P), and temperature (°C) data from the Newman U.S. Geological

Survey Stream Gage (#11273400: San Joaquin River above Merced River near Newman,

California) located just upstream (approximately 100 m) of the net weir.

1.2.4 Fish Identification

We used the silhouettes to identify and classify fish that passed through the Vaki unit as either

Chinook Salmon or “other species”. We presumed that the species identification accuracy of

fishes other than adult Chinook Salmon was likely poor without the addition of a camera unit

working in concert with the Vaki unit. For quality control, silhouettes were independently

6

classified by a minimum of two employees. Silhouettes with conflicting classifications were sent

to Ryan Cutthbert, FISHBIO Oakdale, California for verification.

1.2.5 Calibration Testing

In general, we assumed: (1) that all fish passing the sampling location swam through the Vaki

unit (henceforth referred to as net weir efficiency), (2) the scanner plates recorded every fish

greater than 4 cm in body depth that passed through the Vaki unit (henceforth referred to as

scanner efficiency), and (3) the identification of adult salmon was 100% accurate. Efficiency

testing of the weir was not conducted during 2016 monitoring. However, we conducted pilot

tests to quantify the scanner efficiency and identification accuracy.

Scanner Efficiency.— To determine the efficiency of the Vaki unit scanning fish classified as

“other species”, we conducted a pilot calibration study using known fishes. On June 1 and June

6, 2016, we collected fish in a 200-m reach immediately upstream of the Vaki unit using a 15.24-

m x 1.22-m beach seine with 3.18-mm delta mesh and a fyke net with a closed cod end attached

to the upstream end of the Vaki unit. Fish with a body depth less than 4 cm were not included in

the study because of the scanner settings preclude fish less than 4 cm in body depth from being

recorded. Fish collected were measured (body depth, total length [TL]), had a string lopped

through their mouth and operculum to create a tether, and were forced to pass through the Vaki

unit up to 10 times. The detection of the fish during each passage event was classified as “Read”

when at least one silhouette was recorded or “No Read” when no silhouette was recorded. The

proportion of passage events classified as “Read” to “No Read” was determined for each fish.

Identification Accuracy.— To evaluate our ability to accurately differentiate adult Chinook

Salmon from other fish species, we obtained pairs of silhouettes from 100 fish (60 salmon and 40

other species) recorded by the Vaki unit on Butte Creek, which had their identification confirmed

by camera images. These 100 silhouette pairs were haphazardly combined with 100 silhouette

pairs recorded by our Vaki unit in the Restoration Area. Thereafter, a total of three employees

(i.e., observers) responsible for identifying fish using the Vaki unit data collected within the

Restoration Area were tasked with classifying each of the 200 silhouette pairs as “Chinook

Salmon” or “other species”. We calculated the percent accuracy for each observer using the

silhouettes from fish with known identification from Butte Creek.

1.3 Results

Throughout the monitoring period, the average daily streamflow ranged 3.3–62.6 m3/s (Figures 3

& 4). Two rain events increased streamflow between March 3 and March 20, 2016 (Figure 4).

The river stage increased above the top of the net weir as streamflow exceeded approximately 34

m3/s (Figure 3). After streamflow subsided, we reset and repaired the net weir between March 30

and April 6, 2016. In addition, there was an increase in streamflow on April 12, 2016 that did not

7

correspond with a rain event, which may be associated with either irrigation returns or

wastewater effluent. Median temperatures during the monitoring period ranged 14.8˚C to 27.6˚C

and were recorded in the critical (17–20˚C) and lethal (20˚C) range for adult Chinook Salmon for

54 of the 99 monitoring days (SJRRP 2010). The sampling period concluded and the weir was

removed when minimum daily temperatures exceeded the lethal temperature limit of returning

spring-run Chinook Salmon of 20˚C for 14 consecutive days.

Diode blocks on the scanner plates caused by aquatic vegetation and other debris were common,

occurring during 39 of 99 of monitoring days. Blocks of almost all diodes caused the scanner to

stop recording during an 8-day period from March 30 to April 6, 2016. During this time, we were

unable to access the Vaki unit to troubleshoot diode blocks due to high water until April 6, 2016.

The severe diode blocks were cleared when we moved the scanner plates closer together (April

8, 2016). However, diode blocks at some level returned but were reduced when we added a

shade structure to the Vaki unit tower (late April), fish detections still occurred.

8

Figure 3. The net weir the day after installation on March 4, 2016 when the mean daily discharge

was 9.5 m3/s (A) and the net weir at 35.4 m

3/s on March 8, 2016 (B).

1.3.1 Adult Return Monitoring

A total of 1,715 fish were detected passing through the Vaki unit during the study period (Figure

4). However, no adult Chinook Salmon were identified. On average, fish had a body depth of 8.4

cm (range 4.0–22.0 cm) and a calculated TL of 49.6 cm TL (range 18.0–132.0 cm TL),

indicating that a range of fish sizes was detectable with the Vaki unit including large fish.

Although the net weir structure was compromised from scour and overtopping in stream flows

exceeding 34 m3/s, fish passage through the Vaki unit continued and often increased.

We did observe three Sacramento Splittail Pogonichthys macrolepidotus entangled in the net

weir while attempting to move upstream during the high streamflow on March 8, 2016. The

upstream movement of the Sacramento Splittail was determined by the orientation of the fish

while entangled in the net weir. Additionally, several (n = 11) dead Common Carp Cyprinus

A

B

9

carpio floated downstream and were removed from the net weir throughout April and May.

There is also evidence that White Sturgeon Acipenser transmontanus moved upstream of the net

weir and Vaki unit during the study period. A total of three tagged (V 16 acoustic transmitter,

Vemco©, Bedford, Nova Scotia) White Sturgeon were detected by an acoustic receiver deployed

upstream of the Vaki unit between March 9 and March 14, 2016 (Zac Jackson, Laura

Heironimus, USFWS, personal communication). Although we are unable to confirm the passage

of any White Sturgeon through the Vaki unit, there were fish silhouettes that contain sturgeon-

like profiles that were of similar sizes to the tagged individuals. The identification of these fish

remains unclear and warrants further exploration.

Figure 4. Daily count of fish detections recorded by the Vaki unit and mean daily streamflow

(m3/s) while sampling in the San Joaquin River at Hills Ferry, California from March 3 to June 8,

2016. The vertical dotted line on April 8, 2016 is when the distance between the scanner plates

was reduced from 42.5cm to 25.5cm.

1.3.2 Calibration Testing

Scanner Efficiency Testing.— A total of 22 individual fish, representing nine species, were used

to determine the scanner efficiency of the Vaki unit for fish classified as “other species” (Table

1). Passages were detected on average 37% of the time (range 0–100%). The reduced scanner

visibility during these tests indicated multiple diode blocks on dates of field tests.

10

Table 1. The proportion of passage events containing silhouettes for individual fish of various

sizes captured, tethered, and passed through the Vaki unit on June 1 and June 6, 2016 in the San

Joaquin River, California.

Species TL

(mm)

Body

Depth

(mm)

Passage

Events

(#)

Proportion of passage

events with at least one

silhouette recorded Common Name Scientific Name

Black Crappie Pomoxis nigromaculatus 208 75 4 0.50

Channel Catfish Ictalurus punctatus 448 85 6 0.33

Channel Catfish I. punctatus 374 70 10 0.70

Channel Catfish I. punctatus 675 140 4 1.00

Common Carp Cyprinus carpio 534 138 1 0.00

Common Carp C. carpio 775 260 11 0.36

Common Carp C. carpio 650 195 10 0.40

Goldfish Carrassius auratus 215 80 6 0.33

Largemouth Bass Micropterus salmoides 231 68 6 0.00

Largemouth Bass M. salmoides 236 74 6 0.17




Redear Sunfish Lepomis microlophus 209 80 4 0.25

Spotted Bass M. punctulatus 267 74 6 0.17






Striped Bass Morone saxatilis 254 58 6 0.00

White Catfish Ameirus catus 585 114 8 0.38

Identification Accuracy. — The average fish identification accuracy among the three observers

was 94% (range 86–99%) for all species combined (Table 2). All errors occurred in observers

misidentifying known Chinook Salmon (i.e., representing false negative error), which averaged

9.9% and ranged from 1.7% to 23.0%. The observer with the highest accuracy rate was used as

one of two or more observers to identify the 1,715 fish detected by the Vaki unit.

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Table 2. Identification accuracy among observers of

known Butte Creek Vaki unit and the Program’s Vaki

unit silhouettes.

Species Classification N Observer Accuracy

A B C

Chinook Salmon 60 98% 95% 77%

Other Species 40 0% 0% 0%

All 100 99% 97% 86%

1.4 Discussion

We did not detect any adult spring-run Chinook Salmon returning to the Restoration Area during

our monitoring in 2016. The possible causes for the lack of salmon being detected at Hills Ferry

include incomplete net weir and scanner efficiency, inaccurate fish identification, adults straying

within the Central Valley, and poor survival. Although the exact cause is unknown, we have

evidence to suggest that the efficiency of the net weir and Vaki scanner coupled with poor

juvenile survival may contributed to the lack of adult salmon detected during our monitoring.

Adult Chinook Salmon returns to a particular river is dependent on both the survival of earlier

life-stages and adult stray rates. Because the Program released CWT juveniles from the Feather

River Fish Hatchery into the Restoration Area, the returning individuals may have had a higher

likelihood of straying based on their exposure to multiple water sources before being released

(Palmer-Zwahlen and Kormos 2015; NMFS 2016). However, no CWTs implanted in the fish

released by the Program were recovered at the Feather River Fish Hatchery (Anna Kastner,

California Department of Fish and Wildlife [CDFW], personal communication). Further, no

adipose clipped adult Chinook Salmon were observed by fish monitoring surveys (e.g., snorkel

surveys) in the San Joaquin River basin during the monitoring period (Domenic Giudice, CDFW,

personal communication). Therefore, we do not believe that adults straying were the cause of no

detections of adult salmon at Hills Ferry.

Poor juvenile survival could, in part, account for no adult Chinook Salmon being detected during

our monitoring effort. Out-migrating juveniles move through the San Joaquin River and San

Francisco Estuary where survival is impacted by multiple factors including high water

temperatures, complex water operations, predation, and toxicity (Newman and Brandes 2010;

Perry et al. 2010; Perry et al. 2013; Perry et al. 2016). In dry years, low streamflow

simultaneously intensifies these factors and increases juvenile residence time in these conditions.

In 2014, the San Joaquin River Valley entered the second year of a “Critical” water-year type

designation, the driest classification (CDEC 2016). The year was characterized by reduced

streamflow and high water temperatures. These extreme conditions likely resulted in low

survival of juvenile spring-run released by the Program in 2014. This is consistent with 2014

estimates of less than 5% juvenile survival in the San Francisco Estuary from studies using fall-

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run Chinook Salmon (Buchanan et al. 2017, in prep). Although fall- and spring-run out-

migration periods may be different, survival estimates are likely comparable because both runs

navigated through the same habitat during the critical year type when factors such as high water

temperature, low water velocity, and poor water quality were similar during both migration

periods. Furthermore, poor survival of BY 2013 and BY 2014 spring-run is evident across the

Central Valley where 2016 return estimates to both the Feather River Fish Hatchery and Butte

Creek are among the lowest recorded (Anna Kastner, personal communication; CDFW 2016;

Garman 2016a; Garman 2016b). Evidence of poor juvenile survival and low return rates across

the Central Valley could indicate returns of spring-run to the Restoration Area may also be very

low.

Identification accuracy, as evaluated during the calibration testing, was high. In general, false

negative error rates (i.e., misidentification) greater than 20% can begin to substantially bias fish

identification results (Tyre et al. 2003; Shea et al. 2011). Our observers did not identify “other

species” as a Chinook Salmon and misidentified an average of 9% of the known Chinook

Salmon records. As a result, we presume with high confidence that no adult salmon passed

through the Vaki unit and were misidentified.

Our assumption that all fish moving upstream were directed by the net weir into the Vaki unit

was likely violated during and following the high water event between March 3 and March 20,

2016. During this event, there was incomplete coverage of the channel because (1) the net weir

was underwater, (2) scour created large gaps beneath the net weir, and (3) the river channel

edges extended beyond the net weir into the floodplain. In addition, many sections of the net

weir collapsed based on heavy debris loads bending and displacing the stabilizing t-posts.

Although the Vaki unit was still recording fish silhouettes during the high streamflow event, we

presume that the net weir efficiency was incomplete to an unknown degree.

Incomplete scanner efficiency was evident both during calibration testing and when diode blocks

caused the Vaki unit to shut down for an 8 -day period. Initial tests of the scanner efficiency

indicated that not all fish that passed through the Vaki unit were recorded as a silhouette.

However, the testing was confounded by several factors including not using the target species

(i.e., Chinook Salmon) and low sample sizes with poor representation among local fish species.

Scanner diode malfunction occurred during our tests, which may have been why fish passage

reads were not 100%. Scanner diode blocks were common throughout our monitoring period,

however, detections still occurred on days where diodes were blocked. Minor diode blocks

reduced silhouette quality in some cases and likely resulted in missed fish detections. Nearly

complete diode blocks led the Vaki unit to stop recording any information from March 30 to

April 8, 2016. This time period corresponded to the weir rebuilding phase, however, we presume

fish passage still occurred through the Vaki unit and therefore we underestimated the total

number of fish moving upstream. We recommend that scanner efficiency tests be conducted

during the fall-run Chinook Salmon trap and haul process by adding the Vaki unit to weirs/fykes

capturing salmon. This will produce a dataset of San Joaquin River fall run salmon that could be

13

used to determine efficiency of the scanner and also to provide images for silhouette

identification training and testing.

Because adult salmon returning to the Restoration Area were not detected, management actions

(e.g., adult translocation) were not recommended or conducted for spring-run Chinook Salmon.

As more juvenile spring-run Chinook Salmon are reintroduced into the Restoration Area each

year, the Program anticipates that the number of adults returning to the Restoration Area will

increase. Until restoration projects are completed and volitional passage to suitable holding or

spawning habitat is provided, monitoring adult spring-run Chinook Salmon is needed to assess

the success of the experimental reintroduction of spring-run Chinook Salmon and to inform the

need for management actions such as trapping. We recommend that the Program continue this

passive monitoring for returning adult spring-run Chinook Salmon using a temporary weir and

Vaki unit based on the knowledge garnered during this study. In other river systems, the success

of this passive monitoring gear was proven when they paired with a camera. Species

identification have been confirmed through the digital images as well. We recommend the

Program pair the Vaki unit with a camera system for future studies to enhance fish identification

and detections. Additionally, it is recommended that the Program incorporate an annual

assessment of the detection efficiency of the gear types used (i.e., the weir and the Vaki unit) to

reduce the uncertainty of results presented here and in the future.

14

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Documents

Adult spring-run return monitoring during 2016 …...ii Adult Spring-run Chinook Salmon return monitoring during 2016 within the San Joaquin River, California Prepared by: Judith Barkstedt