Distribution and Joint Fish-Tag Survival of 

Juvenile Chinook Salmon Migrating through the 

Sacramento-San Joaquin River Delta, California, 2008

Open-File Report 2009-1204

Prepared in cooperation with the 

Technical Committee of the Vernalis Adaptive Management Plan and the 

San Joaquin River Group Authority

U.S. Department of the Interior

U.S. Geological Survey

Distribution and Joint Fish-Tag Survival of Juvenile 

Chinook Salmon Migrating through the SacramentoSan Joaquin River Delta, California, 2008 

By Christopher M. Holbrook, Russell W. Perry, and Noah S. Adams 

Prepared in cooperation with the Technical Committee of the Vernalis Adaptive 

Management Plan and the San Joaquin River Group Authority 

Open-File Report 2009–1204 

U.S. Department of the Interior 

U.S. Geological Survey 
U.S. Department of the Interior 

KEN SALAZAR, Secretary 

U.S. Geological Survey 

Suzette M. Kimball, Acting Director 

U.S. Geological Survey, Reston, Virginia: 2009 

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Suggested citation: 

Holbrook, C.M., Perry, R.W., and Adams, N.S., 2009, Distribution and joint fish-tag survival of juvenile 

Chinook salmon migrating through the Sacramento-San Joaquin River Delta, California, 2008: U.S. 

Geological Survey Open-File Report 2009-1204, 30 p. 

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

endorsement by the U.S. Government. 

Although this report is in the public domain, permission must be secured from the individual 

copyright owners to reproduce any copyrighted material contained within this report. 
Contents 

Abstract ......................................................................................................................................................................... 1

Introduction.................................................................................................................................................................... 2

Methods......................................................................................................................................................................... 4

Data Collection........................................................................................................................................................... 4

Fish Handling, Tagging, and Release..................................................................................................................... 4

Acoustic Receivers................................................................................................................................................. 5

Evaluating Tag Failure............................................................................................................................................ 5

Data Analyses............................................................................................................................................................ 6

Travel Times........................................................................................................................................................... 6

Estimating Survival and Migration Route Probabilities ........................................................................................... 6

Parameter Estimation............................................................................................................................................. 8

Population-Level Parameters ................................................................................................................................. 9

Model Selection.................................................................................................................................................... 10

Results......................................................................................................................................................................... 11

Tag Failure............................................................................................................................................................... 11

Travel Times ............................................................................................................................................................ 11

Fish-Tag Survival and Migration Route Probabilities................................................................................................ 14

Fish-Tag Survival for Fish That Traveled through Old River .................................................................................... 15

Fish-Tag Survival for Fish That Traveled through San Joaquin River and Turner Cut ............................................. 15

Entrainment of Tagged Fish into Old River .............................................................................................................. 16

Discussion ................................................................................................................................................................... 16

Entrainment into Old River ....................................................................................................................................... 16

Fish-Tag Survival through the Delta......................................................................................................................... 20

Migration through the Central Delta ......................................................................................................................... 21

Migration Past the Stockton Wastewater Treatment Plant ....................................................................................... 22

Summary ..................................................................................................................................................................... 22

Acknowledgments........................................................................................................................................................ 23

References Cited......................................................................................................................................................... 24

Appendix A. Parameter definitions and estimates ....................................................................................................... 27

iii
Figures 

Figure 1. Schematic of the San Joaquin River and Sacramento-San Joaquin Delta with acoustic 

monitoring and release sites used in the 2008 VAMP study.........................................................................3

Figure 2. Schematic of release-recapture model used to estimate joint fish-tag survival (σhi), detection 

(Phi), route entrainment (Ψhl), and transition (φhi,gj) probabilities for acoustically tagged juvenile Chinook 

salmon released in the San Joaquin River, California, 2008.........................................................................7

Figure 3. (A) Empirical tag survival curve (solid black line; N0 = 66) with theoretical 95-percent confidence 

interval (±1.96 binomial SE) from the tag failure evaluation; and (B) travel time distributions, by release 

week, for tagged fish from release at Durham Ferry to first detection at: (1) the Old River-San Joaquin 

River junction (sites OLD, SJO.n); (2) the Turner Cut-San Joaquin River junction (sites TRN, SJT); (3) the 

State and Federal pumping projects, including the Clifton Court Forebay (sites SWP, CVP, CCFB); (4) 

Jersey Point or Threemile Slough (sites JPT, TMS); and (5) Chipps Island (site MAL) ..............................12

Figure 4. Travel times from release at Durham Ferry to arrival at Chipps Island for tagged fish that 

traveled through the San Joaquin River (Route A; n = 16) and Old River (Route B; n = 15) ......................13

Figure 5. (A) Discharge in the San Joaquin River downstream of the Old River-San Joaquin River junction 

(dashed blue line) and in Old River (solid red line); with (B) fraction of San Joaquin River discharge flowing 

into Old River (solid black line) and cumulative arrival distributions at the Old River-San Joaquin River 

junction for tagged fish released in week 2 at Durham Ferry during the day (solid green line) and night 

(dashed blue line) .......................................................................................................................................17

Figure 6. (A) Arrival distribution at the Old River-San Joaquin River junction and (B) proportion of tagged 

fish (with 95-percent binomial confidence interval) entrained into Old River as a function of the fraction of 

San Joaquin River discharge flowing into Old River at the time of arrival for fish released at Durham Ferry 

in week 2 ....................................................................................................................................................18

Tables 

Table 1. Release group, date, site, time of day, sample size, median fork length, and median weight of 

tagged juvenile Chinook salmon released into the San Joaquin River, California, 2008...............................4

Table 2. Total number of tagged juvenile Chinook salmon detected at five locations in the Delta, with 

proportion that arrived during day and night. ..............................................................................................13

Table 3. Population-level parameter estimates (standard errors in parentheses) with 95-percent profile 

likelihood confidence intervals (C.I.) for tagged juvenile Chinook salmon released in weeks 1 and 2. .......14

iv
Conversion Factors 

Inch/Pound to SI 

Multiply By To obtain 

Flow rate 

cubic foot per second (ft3/s) 0.02832 cubic meter per second (m3/s) 

SI to Inch/Pound 

Multiply By To obtain 

Length 

millimeter (mm) 0.03937 inch (in.) 

meter (m) 3.281 foot (ft) 

kilometer (km) 0.6214 mile (mi) 

Area 

square kilometer (km2) 247.1 acre 

Mass 

gram (g) 0.03527 ounce, avoirdupois (oz) 

Temperature in degrees Celsius (°C) may be converted to degrees Fahrenheit (°F) as follows: 

°F=(1.8×°C)+32 

Concentrations of chemical constituents in water are given either in milligrams per liter (mg/L) or micrograms per 

liter (μg/L). 

v
vi

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Distribution and Joint Fish-Tag Survival of Juvenile 

Chinook Salmon Migrating through the SacramentoSan Joaquin River Delta, California, 2008 

By Christopher M. Holbrook, Russell W. Perry, and Noah S. Adams 

Abstract 

Acoustic telemetry was used to obtain the movement histories of 915 juvenile fall-run 

Chinook salmon (Oncorhynchus tshawytscha) through the lower San Joaquin River and 

Sacramento-San Joaquin Delta, California, in 2008. Data were analyzed within a releaserecapture framework to estimate survival, route distribution, and detection probabilities among 

three migration pathways through the Delta. The pathways included the primary route through 

the San Joaquin River and two less direct routes (Old River and Turner Cut). Strong inferences 

about survival were limited by premature tag failure, but estimates of fish distribution among 

migration routes should be unaffected by tag failure. Based on tag failure tests (N = 66 tags), we 

estimated that only 55–78 percent of the tags used in this study were still functioning when the 

last fish was detected exiting the study area 15 days after release. Due to premature tag failure, 

our “survival” estimates represent the joint probability that both the tag and fish survived, not 

just survival of fish. Low estimates of fish-tag survival could have been caused by fish mortality 

or fish travel times that exceeded the life of the tag, but we were unable to differentiate between 

the two. Fish-tag survival through the Delta (from Durham Ferry to Chipps Island by all routes) 

ranged from 0.05 ± 0.01 (SE) to 0.06 ± 0.01 between the two weekly release groups. Among the 

three migration routes, fish that remained in the San Joaquin River exhibited the highest joint 

fish-tag survival (0.09 ± 0.02) in both weeks, but only 22–33 percent of tagged fish used this 

route, depending on the week of release. Only 4–10 percent (depending on week) of tagged fish 

traveled through Turner Cut, but no tagged fish that used this route were detected exiting the 

Delta. Most fish (63–68 percent, depending on week of release) migrated through Old River, but 

fish-tag survival through this route (0.05 ± 0.01) was only about one-half that of fish that 

remained in the San Joaquin River. Once tagged fish entered Old River, only fish collected at 

two large water conveyance projects and transported through the Delta by truck were detected 

exiting the Delta, suggesting that this route was the only successful migration pathway for fish 

that entered Old River. The rate of entrainment of tagged juvenile salmon into Old River was 

similar to the fraction of San Joaquin River discharge flowing into Old River, which averaged 

63 percent but varied tidally and ranged from 33 to 100 percent daily. Although improvements 

in transmitter battery life are clearly needed, this information will help guide the development of 

future research and monitoring efforts in this system. 

1
Introduction 

Chinook salmon (Oncorhynchus tshawytscha) in California’s Central Valley were 

decimated in the 19th and 20th centuries by overfishing, dam construction, channelization, 

pollution, and water diversions (Clark, 1929; Skinner, 1962, Yoshiyama and others, 1998; 

Williams, 2006). Of the four distinct runs (winter, spring, fall, late fall) present in the Central 

Valley, the winter and spring runs are listed as endangered and threatened, respectively, while 

populations of fall-run Chinook salmon remain the most abundant (Myers and others, 1998; 

Lindley and others, 2004). However, escapement of fall-run salmon recently decreased below 

minimum conservation targets, reaffirming the need for fundamental changes in fisheries and 

water management in the Central Valley (Healey and others, 2008; Lindley and others, 2009). 

The San Joaquin River drains about 83,000 km2

 in California’s Central Valley, and 

along with the Sacramento River, is a primary source of freshwater to San Francisco Bay. Lack 

of recovery of salmon populations in the San Joaquin River has been attributed to diversions and 

water storage dams that reduce river discharge during the spring runoff, when juvenile fall-run 

salmon are actively migrating (The Bay Institute, 2003; Williams, 2006). Flows in the lower San 

Joaquin River are regulated by upstream dams and exports from two water conveyance systems: 

the State Water Project and Central Valley Project. These projects are economically and socially 

important, as they provide water to more than 23 million residents and 3 million acres of 

agricultural land (Healey and others, 2008). Both projects divert water directly from Old River 

(fig. 1). At times, these facilities export all San Joaquin River water (Kimmerer, 2002). Reduced 

water velocities, altered water distribution, increased water temperatures, and reduced turbidity 

can increase mortality of juvenile salmonids through increased exposure to predators and greater 

susceptibility to diseases (Ferguson, 1981; Baker and others, 1995; Smith and others, 2003; 

Marine and Cech, 2004). Fish that arrive at these pumping projects are either entrained into 

water conveyance pumps or screened and collected (that is, “salvaged”) at the fish collection 

facilities. Salvaged fish are then trucked and released into the western Delta near Jersey Point 

(fig. 1; site JPT). Although the export facilities are known to reduce San Joaquin River flows 

and cause direct mortality at the pumps (Kimmerer, 2008), mark-recapture experiments using 

coded wire tags have failed to detect a significant relation between export rates and survival of 

juvenile salmon (Newman and Rice, 2002; Newman, 2008). 

Current management strategies aim to improve survival of juvenile salmon migrating 

from the San Joaquin River through the Sacramento-San Joaquin River Delta (hereafter, “the 

Delta”) by augmenting San Joaquin River discharge and curtailing water exports in the spring 

(San Joaquin River Group Authority, 2009). These management actions have been conducted 

under the auspices of the Vernalis Adaptive Management Plan (VAMP), a long-term research 

program that was established to quantify the effects of alternative management actions on 

juvenile salmon survival. This report presents findings from research on the emigration and 

survival of juvenile salmon conducted under VAMP management actions during spring 2008. 

During this period, San Joaquin River flows were augmented by releases at upstream dams and 

curtailed exports at the pumping projects (for details, see San Joaquin River Group Authority, 

2009). In previous years, a barrier was installed at the head of Old River to reduce the number of 

juvenile salmon exposed to the water pumping projects; but no barrier was installed in 2008. 

2
Figure 1. Schematic of the San Joaquin River and Sacramento-San Joaquin Delta with acoustic 

monitoring and release sites used in the 2008 VAMP study. The number of “ports” represents the number 

of hydrophones at each site. 

The goals of this study were to: (1) estimate route- and reach-specific survival of 

juvenile Chinook salmon migrating from the San Joaquin River through the Delta by each of 

three pathways: the mainstem San Joaquin River (Route A), Old River (Route B), and Turner 

Cut (Route C); (2) quantify route entrainment probabilities at two junctions where fish leave the 

San Joaquin River and enter two alternative migration routes (routes B and C); and (3) describe 

travel times through the study area. Acoustic telemetry was used to obtain movement histories 

for emigrating juvenile Chinook salmon at 16 locations between release in the San Joaquin 

River at Durham Ferry (river km, rkm, 112) and exit from the Delta at Chipps Island (fig. 1), 

including the entrance to Clifton Court Forebay (fig. 1; site CCFB) and the intakes at the State 

Water and Central Valley Projects. Recently, acoustic telemetry techniques have been selected 

over coded wire tags for use in VAMP research due to the very low capture probabilities of 

3
coded wire tags (median capture probability ≤ 0.0008 at the Chipps Island trawl; Newman, 

2008) and the inability to estimate the proportion of fish using different migration routes with 

coded wire tags. In contrast, acoustic telemetry data can be analyzed within a release-recapture 

framework to provide maximum likelihood estimates of survival, route entrainment, and 

detection probabilities with better precision than coded wire tags. 

Methods 

Data Collection 

Fish Handling, Tagging, and Release 

Yearling, fall-run Chinook salmon were obtained from the California Department of Fish 

and Game’s Merced River Hatchery in Snelling, Calif. Fish were anesthetized in a buffered (70 

mg/L NaHCO3) tricane methanosulfonate (70 mg/L) solution, their fork length and weight were 

recorded (table 1), and then acoustic tags (model 795-S; Hydroacoustic Technology, Inc., HTI, 

Seattle, Wash.) were implanted according to procedures outlined by Adams and others (1998) 

and Martinelli and others (1998). The tags were 16.4 mm long, 6.7 mm in diameter, and 

weighed 0.65 g in air, representing 4.3 percent of the mean fish weight (range = 2.3–5.8 

percent). Each tag emitted a unique double-pulsed acoustic signal (2 ms pulse width) every 8.6–

10.0 s and had an expected minimum battery life of 11 days. After tagging, fish were held for 

about 18 h, transported to the release site, and released after being acclimated for 1–3 h in river 

water. Further details on the tagging and release procedures are provided by San Joaquin River 

Group Authority (2009). 

In total, 915 fish were tagged and released (table 1). Releases were divided equally 

between two release periods (weeks 1 and 2), separated by 7 days. Fish were released into the 

San Joaquin River at Durham Ferry and at Windmill Cove (rkm 57) near Stockton (fig. 1). 

Within each release period, about 60 percent of the fish were released at Durham Ferry and 40 

percent were released at Stockton. On each release day, about one-half of the fish were released 

during the day and one-half were released at night. 

Table 1. Release group, date, site, time of day, sample size, median fork length, and median weight of 

tagged juvenile Chinook salmon released into the San Joaquin River, California, 2008. 

 [Ranges are given in parentheses] 

Release 

period Date Release site Time 

Number 

of 

samples 

Median fork 

length, in 

millimeters Median weight, in grams 

Week 1 April 29 Durham Ferry Day 144 109 (103–120) 14.9 (12.1–21.2) 

Night 138 110 (101–125) 15.1 (12.1–22.8) 

May 1 Stockton Day 93 108 (100–117) 14.6 (12.3–20.0) 

Night 94 109 (102–123) 14.5 (12.1–25.4) 

Week 2 May 6 Durham Ferry Day 139 108 (100–122) 14.1 (12.1–20.8) 

Night 144 111 (103–132) 15.6 (11.8–28.7) 

May 8 Stockton Day 85 112 (103–123) 15.3 (12.3–21.8) 

Night 78 110 (102–130) 15.0 (12.1–24.8) 

4
Acoustic Receivers 

Tagged fish were detected in holding tanks at the Merced River Hatchery before 

transport and release. Movements of tagged fish through the study area were monitored by 

autonomous receivers at 16 sites between Durham Ferry and Chipps Island (fig. 1). Fourteen 

sites were monitored using single-hydrophone acoustic receivers (HTI model 295). Due to the 

width of the channel at Jersey Point (site JPT) and Chipps Island (site MAL), receivers with four 

hydrophones (HTI model 291) were used to ensure complete “bank-to-bank” coverage as tagged 

fish passed these locations. All single-hydrophone receivers were maintained by Natural 

Resource Scientists, Inc. (Red Bluff, Calif.). The U.S. Geological Survey (California Water 

Science Center, Sacramento, Calif.) maintained receivers at Jersey Point and Chipps Island. 

Duplicate receivers were installed at seven sites (MAL, JPT, TMS, SJT, TRN, SWP, and CVP) 

to estimate detection probabilities (see section, “Estimating Survival and Migration Route 

Probabilities”). Quantifying detection probabilities using duplicate receivers was particularly 

important at Chipps Island, where survival and detection probabilities would have otherwise 

been confounded because there were no detection sites downstream of Chipps Island. Detections 

at three sites (MID, OSJ, FAL) provided behavioral information, but were not included in the 

release-recapture model because they lacked double detection arrays necessary to estimate 

detection probabilities. 

Acoustic receivers were operated for 24 days after the last fish was released. Detections 

recorded by the receivers were initially identified using an auto-detection routine in the software 

program MarkTags (HTI) and then further validated by visually examining echograms of 

potential detections (Ehrenberg and Steig, 2003). 

Evaluating Tag Failure 

One major assumption of using acoustic tags to estimate survival is that all surviving fish 

exit the study area (that is, pass Chipps Island) with functioning tags. Premature tag failure, 

defined as failure of any tag before a live fish passes Chipps Island, will negatively bias survival 

estimates (that is, true survival will be greater than estimated survival) because release-recapture 

models will interpret tag failure as fish mortality. We tested 66 tags in a closed system to 

quantify the rate of tag failure over time. Tags were continuously monitored with an acoustic 

telemetry receiver (HTI model 290) in a water-filled tank until all tags ceased to operate. 

Because water temperature affects the life expectancy of the tag, we controlled water 

temperature in the tank (ranged from 15 to 21°C during the study period) to mimic the daily 

mean water temperature in the San Joaquin River at Jersey Point (data obtained from 

http://cdec.water.ca.gov/; accessed April 2009). The time-to-failure of each tag was calculated 

as the elapsed time between initiation and final detection. We constructed an empirical 

cumulative distribution function from the time-to-failure data to estimate the probability that any 

tag survived to a given date. 

5
Data Analyses 

Travel Times 

The travel time for each tagged fish between release and any downstream monitoring 

site was calculated as the elapsed time between release and first detection at the downstream 

site. Individual travel times were calculated from release to (1) the Old River-San Joaquin River 

junction (sites SJO and OLD); (2) the Turner Cut-San Joaquin River junction (sites SJT and 

TRN); (3) water export facilities (sites CCFB, SWP, and CVP, collectively); (4) Jersey Point 

and Threemile Slough (sites JPT and TMS); and (5) Chipps Island (site MAL). We present plots 

of travel time distributions and differences in median travel times (DM) between various groups 

(for example, weeks 1 and 2, routes A and B). Due to tag failure, the true median travel times 

probably are longer than we observed. We did not test for travel time differences among weeks 

or sites because travel times, like fish survival estimates, are negatively biased due to premature 

tag failure. 

Estimating Survival and Migration Route Probabilities 

Following the framework presented by Perry and others (in press), we developed a 

multi-state release-recapture model to estimate detection (Phi), route entrainment (Ψhl), survival 

(Shi), and transition probabilities (φhi,gj ; see Brownie and others, 1993 and Skalski and others, 

2002). The full model (fig. 2) consisted of 3 migration routes (A, B, C), 2 groups (Durham 

Ferry, Stockton), and 68 parameters: 2 tag survival probabilities, 16 joint fish-tag survival 

probabilities, 2 route entrainment probabilities, 20 transition probabilities, and 28 detection 

probabilities (see appendix A, table A1 for parameter definitions). Detection probabilities (Phi) 

estimate the probability that a tagged fish is detected at site hi (h = a, b, c, d, e) given that the 

fish survives to site hi with an operational tag. Route entrainment probabilities (Ψhl) estimate the 

probability of a fish entering channel h at junction l (l= 1, 2) given that the fish survives to 

junction l. Survival probabilities (Shi) estimate the probability that a tagged fish survives from 

site hi to the next downstream site. 

A branching process was used to model entrainment probabilities into Old River and 

Turner Cut. At the first junction (Old River-San Joaquin River junction), Ψa1 estimates the 

probability that a fish remains in the San Joaquin River. Conversely, Ψb1 = (1- Ψa1) estimates the 

probability that a fish is entrained into Old River at this location. At the second junction (Turner 

Cut-San Joaquin River junction), Ψa2 estimates the probability of a fish remaining in the San 

Joaquin River, and Ψc2 = (1- Ψa2) estimates the probability that a fish is entrained into Turner 

Cut at this location. 

6
φc1, e1

φ c1, d1

σb2

σa1

Pa2 SJO.s

σa2

 a1 b1 = (1- a1)

σa3

SJO.n

STP.s

OLD

STP.n

Pa3

Pa4

Pa5

Pb1

 a2 c2 = (1-  a2)

Pa6 SJT Pc1 TRN

Pa7 JPT Pb2 CVP

MAL

σa7 σb3

Pa8

σd1

Pd1

Pb3

Pe1 TMS

σe1

SWP

CCFB

φ b1, b2

φ b1, a7

φ b1, d1

φ b1, e1

σb1 = ∑

φ c1, b2

φ c1, a7 σc1 = ∑ φ a6, b2

φ a6, a7

φ a6, d1

φ a6, e1

σa6 = ∑

Sa0, DF

Pa1, DF

Tag Implanted

Release at 

Durham Ferry

MRH

σa4

σa5, DF

Release at 

Stockton

Sa0, ST

Pa1, ST

Tag Implanted

MRH

σa5, ST

Figure 2. Schematic of release-recapture model used to estimate joint fish-tag survival (σhi), detection 

(Phi), route entrainment (Ψhl), and transition (φhi,gj) probabilities for acoustically tagged juvenile Chinook 

salmon released in the San Joaquin River, California, 2008. Horizontal bars represent detection stations. 

7
In the lower Delta, fish could exit some reaches at multiple locations by taking different 

migration pathways through unmonitored river junctions. In these situations, it is impossible to 

estimate separately the probability of taking each pathway from the probability of survival in a 

particular pathway. Thus, transition probabilities (φhi,gj) estimate the joint probability of 

surviving between hi and gj and taking a migration pathway connecting site hi to gj. Although 

biological interpretation of an individual φhi,gj is difficult, the sum of all φhi,gj over all exit 

locations (gj) for a given hi yields the probability of survival from site hi to all possible exit sites 

from this reach (Brownie and others, 1993). Parameter estimates will be unbiased if all model 

assumptions are satisfied (Burnham and others, 1987; Skalski and others, 2002). The tag failure 

trial was specifically designed to test the assumption that each tag remained operational during 

migration of fish through the study area. However, results from the tag failure trial revealed that 

this assumption was not satisfied (see section, “Results”), yielding negatively biased estimates 

of Shi. 

When tag failure (or tag loss) is present in mark-recapture data, each estimate of survival 

actually represents the combined probability of tag “survival” and fish survival: 

hi hi hi ,tag ,fish   S S (1) 

Where Shi,tag and Shi,fish are the survival probabilities for the tag and the fish, and hi is the joint 

probability that both the tag and fish survive from site hi to the next downstream site. Eqn. 1 

shows that only when Shi,tag = 1 (that is, zero probability of tag failure) will hi = Shi,fish, 

providing an unbiased estimate of fish survival. Because we estimated that Shi,tag < 1 in this 

study, we report hi to explicitly indicate that these estimates represent the joint probability of 

both fish and tag survival (hereafter, “fish-tag survival”). Although a low estimate of hi can not 

be interpreted as low fish survival alone, it does indicate some combination of fish mortality and 

travel times that exceeded the life of the tag. 

One novel aspect of this model is that detections in holding tanks at Merced River 

Hatchery (site MRH) were included in the detection history, which allows estimation of Pa1, the 

detection probability in holding tanks during the hour prior to transport, and Sa0, the probability 

of tag survival between implantation and release. In essence, Sa0 estimates the proportion of 

functioning tags at release and prevents bias associated with tag failure in the hatchery from 

estimates of in-river survival in the first reach. 

Parameter Estimation 

We used maximum likelihood techniques to estimate parameters based on a multinomial 

probability model that categorized each fish into a mutually exclusive and exhaustive detection 

history. Perry and others (in press) provide a concise explanation of the detection histories used 

in this type of model. There were 1,400 possible unique detection histories for fish released at 

Durham Ferry and 84 possible unique detection histories for fish released at Stockton. Each 

detection history represents one cell of a multinomial distribution where the probability of each 

cell is defined as a function of the detection, fish-tag survival, route entrainment, and transition 

probabilities (for details, see Perry and others, in press). 

8
Given the cell probabilities, the maximum likelihood estimates are found by maximizing 

the likelihood function of a multinomial distribution with respect to the parameters: 

  1

, jkm

J n

km km jkm jkm

j

L Rn    (2) 

where Lkm is the likelihood for the kth release group (k = week 1, week 2) at the mth release site 

(m = Durham Ferry (DF), Stockton (ST)), R is the number of fish released, nj is the number of 

fish with the jth detection history, and πj is the probability of the jth detection history expressed 

as a function of the parameters ( 



). Auxiliary likelihoods were used to estimate the detection 

probabilities at the double-detection array at Chipps Island, as described by Skalski and others 

(2002). Auxiliary likelihoods were not used to estimate detection probabilities at other doubledetection sites because detection histories indicated that detection probabilities at these and 

many other sites were equal to 1.0 (see appendix A, table A2). Similarly, transition and fish-tag 

survival probabilities were set to 0 or 1 where appropriate. The likelihood was numerically 

maximized with respect to the parameters using the software program USER (Lady and others, 

2008). Parameters were estimated separately for each release week (k) but simultaneously for 

both release sites (m) by expressing the joint likelihood as the product of Lk,DF and Lk,ST. We 

examined Anscombe residuals (McCullah and Nelder, 1983) to assess goodness of fit for each 

full model. 

Population-Level Parameters 

Population-level parameters were estimated as combinations of reach- and route-specific 

parameters estimated by the model. Migration route probabilities (Ψr) represent the probability 

that any tagged fish used migration route r (r = A, B, C), and were estimated as functions of 

route entrainment probabilities: 

;  ΨΨΨ a2a1A (3) 

Ψ B  (1 Ψa1 )  Ψb1 ; and (4) 

. a1C a2 ΨΨ c2a1 ΨΨ (1 Ψ )  (5) 

Route survival probabilities (σr) represent the probability that a tagged fish survived with a 

functioning tag from Durham Ferry to Chipps Island, given that it entered route r. When route 

entrainment probabilities are estimated at every junction, fish-tag survival between Durham 

Ferry and Chipps Island is simply the product of all survival probabilities that trace each 

migration path through the Delta (Perry and others, in press). However, when the model 

includes transition probabilities (φhi,gj) survival through each migration path must account for all 

possible pathways where transition probabilities are estimated. Thus, fish-tag survival 

probabilities were derived for each route as: 

σσσσσσ ( σσσσσ );  e1e1a6,a5a4a3a2a1A   a7a7a6,   b3b2b2a6,   d1d1a6,  (6) 

 σσσ ( e1e1b1,a2a1B   a7a7b1,   b3b2b2b1,   σσσσσ d1d1b1, ); and (7) 

σσσσσσ ( σσσσσ ).  e1e1c1,a5a4a3a2a1C   a7a7c1,   b3b2b2c1,   d1d1c1,  (8) 

9
Total fish-tag survival through the Delta among all routes (σDelta) was calculated as the sum of 

fish-tag survival among all routes, weighted by each migration route probability: 

. Delta CCBBAA    σΨσΨσΨσ (9) 

We used the “Delta” method (Seber, 1982) to estimate the standard error for derived parameters. 

Profile likelihood 95-percent confidence intervals also were estimated (appendix A, table A2). 

Model Selection 

Releases at Stockton were intended to supplement sample sizes in the lower mainstem 

San Joaquin River. Ideally, detection, survival, route entrainment, and transition probabilities 

could be pooled between the two releases to increase precision of each parameter estimate. 

Pooling among releases, however, assumes that survival and route entrainment probabilities are 

equal between fish released at each site. Therefore, we used Akaike’s information criterion 

(AIC) to test whether parameters could be assumed equal between release sites (Burnham and 

Anderson, 2002). Among candidate models, the model with the smallest AIC value represents 

the model with the most favorable tradeoff between precision and accuracy of the estimates (that 

is, over-fitting versus under-fitting). The difference in AIC values (ΔAIC) between two models 

represents the degree of support for one model over another (Burnham and Anderson, 2002). As 

a general rule, ΔAIC < 2 indicates little or no evidence that either model is more appropriate than 

the other model. Thus, when ΔAIC ≥ 2, we selected the model with the smallest AIC value, but 

when ΔAIC < 2, we selected the model with the fewest number of parameters. We selected the 

model with the fewest parameters when ΔAIC < 2 in order to simplify presentation of the results 

with the assumption that this would have minimal affect on resulting estimates. 

Three candidate models were developed for each release period. Under the full model 

(Model 1: PimσimΨimφim), all parameters were estimated separately for each monitoring site i and 

release site m. In the first reduced model, each detection probability was set equal between the 

two release sites (Model 2: Pi·σimΨimφim). If Model 2 was selected over Model 1, then each 

detection, fish-tag survival, route entrainment, and transition probability was set equal between 

the two release sites in the final candidate model (Model 3: Pi·σi·Ψi·φi·). If Model 1 was selected 

over Model 2, then all detection probabilities were estimated separately in the final model, but 

each fish-tag survival, route entrainment, and transition probability was set equal between the 

two release sites (Model 3: Pimσi·Ψi·φi·). We never set Sa0 or Pa1 equal between release sites 

because these parameters were not used to estimate population-level parameters. We never set 

σ5 equal between release sites because the Stockton release site was located within this reach. 

For the same reason, all population-level parameters, where appropriate, were estimated with σ5, 

DF and never with σ5, ST. 

10
Results 

Tag Failure 

 All test tags in the extinction trial expired within 20 days of initialization (fig. 3A; see 

San Joaquin River Group Authority, 2009). Test tags showed steady failure of about 2 percent 

per day between days 1 and 15, followed by rapid expiration between days 15 and 20. The 

estimated probability of tag survival to the start of day 12 (that is, expected minimum tag life) 

was 0.79 ± 0.05 (binomial SE). We estimate that 55–78 percent (95-percent confidence interval) 

of the tags were still functioning when the last fish was detected at Chipps Island, 15 days after 

release. 

Travel Times 

Tagged fish predominantly arrived at monitoring sites during daylight (table 2). Most 

tagged fish reached the Old River-San Joaquin River junction within 1.5 days after release at 

Durham Ferry (fig. 3B), but took 2–8 days after release to reach the Turner Cut-San Joaquin 

River junction. Tagged fish reached the pumping facilities faster than they reached the Turner 

Cut-San Joaquin River junction (DM = 1.76 days). Fish reached Jersey Point (DM = 2.95 days) 

and Chipps Island (DM = 2.81 days) faster after release in week 2 compared to week 1, but much 

smaller differences were observed between weeks at the Old River-San Joaquin River junction 

(DM = 0.03 days) and the pumping facilities (DM = 0.08 days). 

Fish released at Durham Ferry arrived at Chipps Island 2.9–14.9 days (median 8.8 days) 

after release in week 1, and 2.5–11.3 days (median 5.6 days) after release in week 2. Fish 

released at Stockton arrived at Chipps Island 5.6–11.3 days (median 8.3 days) after release 

during week 1, and 3.3–13.3 days (median 5.3 days) after release during week 2. Although 

sample sizes were small, tagged fish that traveled through Old River (Route B) reached Chipps 

Island (by salvage and trucking) faster than fish that traveled through the mainstem San Joaquin 

River past both junctions (Route A; fig. 4; DM = 3.68 d). Travel times were not available for 

tagged fish that traveled through Turner Cut (Route C) because none of the 49 tagged fish 

detected in this route were detected at Chipps Island. 

11
0.0 0.2 0.4 0.6 0.8 1.0

(n=15)

(n=16)

(n=15)

(n=19)

(n=70)

(n=83)

(n=29)

(n=28)

(n=218)

(n=197)

MAL

JPT, TMS

SWP, CVP

TRN, SJT

OLD, SJO.n

0 1 2 3 4 5 6 7 8 9 10 12 14 16 18 20

Week 1

Week 2

Proportion of Tags Active

Monitoring Location

A)

B)

Days Since Release

Figure 3. (A) Empirical tag survival curve (solid black line; N0 = 66) with theoretical 95-percent confidence 

interval (±1.96 binomial SE) from the tag failure evaluation; and (B) travel time distributions, by release 

week, for tagged fish from release at Durham Ferry to first detection at: (1) the Old River-San Joaquin 

River junction (sites OLD, SJO.n); (2) the Turner Cut-San Joaquin River junction (sites TRN, SJT); (3) the 

State and Federal pumping projects, including the Clifton Court Forebay (sites SWP, CVP, CCFB); (4) 

Jersey Point or Threemile Slough (sites JPT, TMS); and (5) Chipps Island (site MAL). Sample sizes 

(numbers of fish detected) are shown at right. Box shows median, 25th and 75th percentiles. Whiskers 

extend to 1.5 times the interquartile range. Symbols show observations greater than 1.5 times the 

interquartile range. 

12
Table 2. Total number of tagged juvenile Chinook salmon detected at five locations in the Delta, with 

proportion that arrived during day and night. 

[Daylight was defined as the period between morning and evening civil twilights at Stockton, 

Calif., for each day. Daily civil twilight data were obtained from <http://www.usno.navy.mil/>.] 

Release 

site(s) Monitoring location Monitoring sites 

Total 

number Percentage of day Percentage of night 

Durham Ferry Old R.-San Joaquin R. 

Junction 

OLD 

SJO 

415 94.2 5.8 

Durham Ferry Turner Cut-San Joaquin 

R. Junction 

TRN 

SJT 

57 82.5 17.5 

Stockton Turner Cut-San Joaquin 

R. Junction 

TRN 

SJT 

212 76.0 24.0 

Durham Ferry Water Pumping Facilities SWP 

CCFB 

CVP 

153 71.9 28.1 

Durham Ferry 

and Stockton 

Chipps Island MAL 72 86.1 13.9 

Travel time (d) to Chipps Island

Migration Route

0 5 10 15 20

A B

Figure 4. Travel times from release at Durham Ferry to arrival at Chipps Island for tagged fish that 

traveled through the San Joaquin River (Route A; n = 16) and Old River (Route B; n = 15). Route C is not 

shown due to insufficient data (n = 0). Box shows median, 25th and 75th percentiles. Whiskers extend to 

minimum and maximum. 

13
Fish-Tag Survival and Migration Route Probabilities 

We found little evidence of overdispersion (that is, greater variability in the data than 

expected under the model), as only 1 of the 2,980 encounter history frequencies (across both 

weeks) was more extreme than expected given the fitted model estimates (that is, the absolute 

value of the Anscombe residual was greater than 1.96). Although the residual for the encounter 

history was 2.71, only two individuals were observed with this history for which 0.15 

individuals were expected. For week 1, the AIC values were 283.0, 278.3, and 279.1 for models 

1 (PimσimΨimφim), 2 (Pi·σimΨimφim), and 3 (Pi·σi·Ψi·φi·), respectively. Among these, we selected 

Model 3 because ΔAIC = 0.8 and Model 3 had the fewest parameters (29 versus 32). For week 2, 

the AIC values were 200.00, 203.4, and 198.3 for models 1 (PimσimΨimφim), 2 (Pi·σimΨimφim), and 

3 (Pimσi·Ψi·φi·), respectively. Among these, we selected Model 3 because it had the smallest AIC 

value and fewest parameters (29 versus 32). Note that the selected model (Model 3) differs 

between the 2 weeks. Although fish-tag survival and route entrainment probabilities were set 

equal between release sites for both weeks, we set all detection probabilities equal between 

release groups in week 1, but not week 2. 

Fish-tag survival probabilities through the Delta (σDelta) were 0.06 ± 0.01 (SE) and 0.05 ± 

0.01 for weeks 1 and 2, respectively (table 3). Most tagged fish traveled through Old River 

(Route B; ΨB = 0.68 and 0.63 in weeks 1 and 2, respectively) and were salvaged and trucked. 

Fewer fish traveled through the San Joaquin River (Route A) past both junctions (ΨA = 0.22 and 

0.33), and a small proportion of the fish traveled through Turner Cut (Route C; ΨC = 0.10 and 

0.04). Fish-tag survivals for each route were consistent between weeks (table 3) and were 

highest for Route A (σA = 0.09 ± 0.01), lower for Route B (σB = 0.05 ± 0.02), and lowest for 

Route C (σC = 0.00). 

Table 3. Population-level parameter estimates (standard errors in parentheses) with 95-percent profile 

likelihood confidence intervals (C.I.) for tagged juvenile Chinook salmon released in weeks 1 and 2. 

Week 1 Week 2 

Parameter 

Estimate 

(SE) 95% C. I. 

Estimate 

(SE) 95% C. I. σDelta 0.053 (0.013) 0.032, 0.082 0.061 (0.012) 0.040, 0.089 

σA 0.094 (0.024) 0.056, 0.149 0.092 (0.019) 0.059, 0.135 

σB 0.048 (0.017) 0.022, 0.088 0.048 (0.017) 0.022, 0.088 

σC 0.001 (0.001) 0.000, 0.005 0.000 

ΨA 0.215 (0.029) 0.162, 0.277 0.333 (0.032) 0.274, 0.397 

ΨB 0.681 (0.038) 0.605, 0.752 0.625 (0.034) 0.558, 0.689 

ΨC 0.103 (0.019) 0.071, 0.145 0.041 (0.011) 0.023, 0.067 

14
Fish-Tag Survival for Fish That Traveled through Old River 

Within Route B, fish-tag survival was lowest through the three reaches associated with 

the pumping projects: the Clifton Court Forebay (σb2 = 0.37 ± 0.09 and 0.39 ± 0.10 for weeks 1 

and 2); the State Water Project (σb3 = 0.16 ± 0.10 and 0.47 ± 0.15); and the Central Valley 

Project (σb2 = 0.11 ± 0.05 and 0.05 ± 0.04). Estimated transition probabilities from Old River to 

Jersey Point (site JPT) and Threemile Slough (φb1,e1 and φb1,a7) were not greater than 0.01 for 

either week (appendix A, table A2), indicating that tagged fish that traveled through Old River 

either exclusively reached Chipps Island (that is, exited the Delta) through the collection 

facilities at the pumping projects (including transport) or that none of the fish that traveled 

through Old River traversed the central Delta with a functioning tag. Of all tagged fish detected 

in Old River (site OLD; Route B), only 2 percent (4 of 187) were later detected at the secondary 

sites (1 at MID, 3 at FAL). 

Fish-Tag Survival for Fish That Traveled through San Joaquin River and Turner Cut 

Routes A and C have three reaches in common between the Old River and Turner Cut 

junctions (figs. 1 and 2). Among these, fish-tag survival was lowest in the reach between site 

STP.n and the Turner Cut-San Joaquin River junction (σa5, DF = 0.49 ± 0.07 and 0.56 ± 0.07 for 

weeks 1 and 2). Although similar in size, fish-tag survival was higher (compared to σa5, DF) in 

the reach that extended from the Old River-San Joaquin River junction to site STP.s (σa3 = 0.85 

± 0.05 and 0.70 ± 0.05). Estimated fish-tag survival through the reach containing the Stockton 

Wastewater Treatment Plant (σa4) were 0.96 ± 0.03 in week 1 and 0.89 ± 0.05 in week 2 

(appendix A, table A2). 

Lower fish-tag survival for Route C (σC = 0.00) compared to Route A (σA = 0.09) can be 

attributed to low fish-tag survival (σc1 = 0.03 ± 0.03 and 0.00 for weeks 1 and 2) between the 

entrance to Turner Cut and any of the next monitoring sites (JPT, TMS, CCFB, SWP, or CVP). 

Similarly, of all tagged fish detected in Turner Cut (site TRN; Route C), only 4 percent (2 of 49; 

both at site MID) were later detected at any of the three sites that were not included in the 

release-recapture model. 

For fish that survived to the junction of Turner Cut, the estimated probabilities of 

entrainment into Turner Cut were 0.32 ± 0.05 for week 1 and 0.11 ± 0.03 for week 2. Thus, most 

tagged fish remained in the San Joaquin River at its junction with Turner Cut. Transition 

probabilities from the San Joaquin River near Turner Cut to the pumping projects (φa6,d1 and 

φa6,b2) were zero, indicating that tagged fish that traveled through Route A did not enter routes 

leading to the pumping projects, or that none of the tagged fish that used this route traversed the 

central Delta with a functioning tag. However, of all fish detected in the San Joaquin River 

below its junction with Turner Cut (site SJT; Route A) 22 percent (40 of 186; 24 at MID, 6 at 

OSJ, 10 at FAL) were later detected at the three sites that were not included in the releaserecapture model. This suggests that some fish that traveled through Route A entered the central 

Delta, but none reached the pumping projects alive or with a functioning tag. 

15
Entrainment of Tagged Fish into Old River 

Old River discharge was inversely related to discharge in the San Joaquin River 

downstream of the Old River-San Joaquin River junction (fig. 5A). The mean fraction of San 

Joaquin River discharge flowing into Old River at the Old River-San Joaquin River junction was 

63 percent between April 29 and May 13, 2008 (that is, the period when tagged fish arrived at 

this location) and ranged from 33 to 100 percent. During the strongest flood tide each day, 100 

percent of the San Joaquin River discharge flowed into Old River (fig. 5B). During this time, the 

San Joaquin River flow reversed direction downstream of the head of Old River, but maintained 

constant downstream flow upstream of the head of Old River. As little as 33 percent of the San 

Joaquin River discharge flowed into Old River during the strongest ebb tide each day. Most 

tagged fish arrived at the head of Old River when flows were either 40–50 percent or 90–100% 

(figs. 5 and 6A). Although the flow distribution was bimodal over the fish arrival distribution, 

the proportion of tagged fish entrained into Old River (Route B) was similar to the fraction of 

the San Joaquin River discharge flowing into Old River at the time of arrival (fig. 6B). 

Discussion 

Although unbiased estimates of fish survival could not be obtained, this study succeeded 

in estimating many important components of migration dynamics that would have been difficult 

to measure using other methods (for example, coded wire tags). For example, most juvenile 

salmon traveled through Old River and were entrained into Old River at a rate similar to the 

fraction of San Joaquin River discharge flowing into Old River. Unlike fish survival estimates, 

entrainment and migration route probabilities obtained from these data are unlikely to be biased. 

Despite wide flow variation within each day, flow dynamics were similar among days 

throughout the study (see San Joaquin River Group Authority, 2009). Thus, estimates of 

entrainment and migration route probabilities probably were not affected by either long travel 

times or tag failures. 

Entrainment into Old River 

It is widely hypothesized that fish are distributed among routes at a junction in 

proportion to the fraction of water flowing into each route. Indeed, the fraction of San Joaquin 

River discharge flowing into Old River during the study period (63 percent) was very similar to 

the overall proportion of fish that were entrained into Old River (68 and 63 percent for weeks 1 

and 2; appendix A, table A2). However, the fraction of San Joaquin River discharge flowing 

into Old River was highly variable within each day, ranging from 33 to 100 percent (fig. 5B). 

We were unable to model (for example, with logistic regression) the proportion of fish entrained 

into Old River as a continuous function of discharge flowing into Old River because the fish 

arrival distribution occurred over a very limited range of the flow distribution and detection 

probabilities were less than 1.0 at this location. Most fish arrived when either 40–50 percent or 

90–100 percent of the San Joaquin River discharge was flowing into Old River (fig. 6A). Still, 

these data show that most tagged fish were entrained into Old River at a rate similar to the 

fraction of San Joaquin River discharge that flowed into Old River when each fish arrived at the 

junction (fig. 6B). 

16
 

Discharge, CFS

-1000 0 1000 2000

Proportion

127.25 127.50 127.75 128.00 128.25 128.50 128.75 129.00 129.25

0.00 0.25 0.50 0.75 1.00

Date and time, 2008

A)

B)

12:00

5/6 

6:00

5/6 

18:00

5/6 

00:00

5/7 

06:00

5/7 

12:00

5/7 

18:00

5/7 

00:00

5/8 

06:00

5/8 

Day Night Night Day

Figure 5. (A) Discharge in the San Joaquin River downstream of the Old River-San Joaquin River junction 

(dashed blue line) and in Old River (solid red line); with (B) fraction of San Joaquin River discharge flowing 

into Old River (solid black line) and cumulative arrival distributions at the Old River-San Joaquin River 

junction for tagged fish released in week 2 at Durham Ferry during the day (solid green line) and night 

(dashed blue line). Arrows indicate date and time of release at Durham Ferry during the day and night. 

Discharge data were obtained from <http://cdec.water.ca.gov/>. Old River discharge was measured at 

CDEC station OH1, located in Old River about 250 m downstream of the Old River-San Joaquin River 

junction. Total San Joaquin River discharge at the Old River-San Joaquin River junction was estimated as 

the sum of discharge at OH1 and in the San Joaquin River near Lathrop (CDEC station SJL; located about 

450 m downstream of the Old River-San Joaquin River junction). 

17
Proportion of All Detected Fish

0.00 0.25 0.50 0.75 1.00

Fraction of San Joaquin R. Flowing into Old River

Proportion of Tagged Fish Entrained into Old River

14

149

9

1

7

1

37

0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0

0.0 0.2 0.4 0.6 0.8 1.0

A)

B)

Proportion of All Detected Fish

0.00 0.25 0.50 0.75 1.00

Fraction of San Joaquin R. Flowing into Old River

Proportion of Tagged Fish Entrained into Old River

14

149

9

1

7

1

37

0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0

0.0 0.2 0.4 0.6 0.8 1.0

A)

B)

Figure 6. (A) Arrival distribution at the Old River-San Joaquin River junction and (B) proportion of tagged 

fish (with 95-percent binomial confidence interval) entrained into Old River as a function of the fraction of 

San Joaquin River discharge flowing into Old River at the time of arrival for fish released at Durham Ferry 

in week 2. The reference line shows where the proportion of fish entrained is equal to the fraction of San 

Joaquin River discharge flowing into Old River. Sample sizes are given for each data point. 

18
The “as-measured” discharge was used in these analyses, not the tidally averaged 

discharge that is most commonly used in a management context. Thus, time of arrival of fish in 

the junction with respect to tidal current phase, as it is mediated by export operations, is 

important in determining entrainment of juvenile salmon into Old River. In lieu of a barrier 

(physical or non-physical), an effective way to prevent fish from entering Old River may be to 

minimize exports at specific times to reduce the proportion of the San Joaquin River discharge 

flowing into Old River when most juvenile salmon are arriving at the Old River-San Joaquin 

River junction (for example, during the day and possibly during flood tides). Changes in exports 

would need to be timed so that desired changes in flows at the head of Old River would occur at 

desired times. The appropriate timing (for example, how long it takes for a change in Clifton 

Court operations to change flows at the head of Old River) and magnitude of the changes could 

be deduced from modeling studies and tested in the field using the existing flow station network. 

In previous years, a physical barrier was installed into the head of Old River to minimize 

entrainment of juvenile salmon into the State and Federal pumping projects. Previous studies 

showed that the barrier improved survival of juvenile salmon migrating through the San Joaquin 

River (Brandes and McLain, 2001). However, because the physical barrier reduced the 

discharge in Old River, it was considered a threat to the endangered Delta smelt (Hypomesus 

transpacificus) and its installation was prohibited starting in 2008. Although physical barriers 

are no longer permitted, non-physical barriers are currently being tested at this site (P. Brandes, 

U.S. Fish and Wildlife Service, oral commun., 2009). Consistent with previous studies (San 

Joaquin River Group Authority, 2008) tagged fish in this study arrived at the Old River-San 

Joaquin River junction almost exclusively during the day (table 2). Future barriers may only 

need to be effective during the day at this time of year to deter most juvenile salmon from 

entering Old River. Managers should consider, however, that diel activity patterns in juvenile 

salmon are known to change in response to varying environmental conditions (see Wilder and 

Ingram, 2006, and references therein). 

It also is important to recognize that release timing may have influenced when fish 

arrived at the Old River-San Joaquin River junction in this study. The narrow range of arrival 

times (fig. 3B) suggests that release timing may have affected arrival timing at this location and 

could have resulted in observed behaviors that are not representative of the run-of-river 

population. For example, many fish released during the day in week 2 arrived at the Old RiverSan Joaquin River junction when 100 percent of San Joaquin River discharge was flowing into 

Old River, but none of the fish that were released at night arrived during this condition (fig. 5B). 

To best represent arrival times of the untagged population, future studies may benefit from an 

intermittent release strategy, where fish are released in smaller groups throughout the day and 

night, rather than in a few discrete bulk releases. Releasing fish farther upstream also may result 

in more “natural” behavior as tagged fish approach the Delta. 

19
Episodic failures of acoustic monitoring equipment also can affect the ability to assess 

fish entrainment relative to other factors, such as the proportion of San Joaquin River discharge 

flowing into Old River at the Old River-San Joaquin River junction. For example, when a 

receiver is not operating properly in one route at a junction, but continues to function in the 

other route, analyses that quantify the relation between a covariate (for example, proportional 

flow) and the probability of entrainment when each fish arrives at a junction are not appropriate 

because one route is underrepresented in the data (that is, P < 1.0). This was the case during 

week 1, when detection probabilities were low in Route B (Pb1 = 0.47) but high in Route A (Pa3

= 0.98) at the Old River-River San Joaquin River junction. The detection probability in Route B 

was higher (Pb1 = 0.94) during week 2 than week 1. Thus, we only included fish released in 

week 2 in our analysis of entrainment into Old River as a function of the fraction of San Joaquin 

River discharge flowing into Old River. 

Fish-Tag Survival through the Delta 

This study also highlights the importance of study-specific tag failure data to explicitly 

test for premature tag failure. In the absence of tag failure data, one must assume that tag failure 

does not occur prior to fish exiting the study region. In this study, fish survival would have been 

underestimated had we not explicitly assessed this assumption. Corrections for bias due to tag 

failure exist (Cowan and Schwarz, 2005. Townsend and others, 2006) but assume that the 

estimated travel time distribution is unbiased. Because the travel time distribution also is 

negatively biased due to tag failure in this study, we could not adjust the survival estimates to 

account for tag failure and do not advocate management actions based solely on the results of 

this study. Nonetheless, the fish-tag survival probabilities obtained in this study are informative, 

as low estimates indicate either mortality or travel times that exceeded the life of the tag. 

Fish-tag survival through the Delta was consistent among weeks (σDelta = 0.05 and 0.06; 

table 3), but much lower than survival reported by Perry and others (in press) for tagged 

Sacramento River juvenile salmon migrating through the Delta. Among the three routes, fish 

that traveled through the San Joaquin River (Route A) past the first two junctions showed the 

highest fish-tag survival (σA = 0.09 in both weeks), but only 22–33 percent of the study 

population used this route (ΨA) among weeks. Conversely, most of the fish (63–68 percent range 

between weeks) traveled through Old River (ΨB), where estimated fish-tag survival (σB = 0.05) 

was about one-half that of Route A. Only 4 and 10 percent of tagged fish traveled through 

Turner Cut (ΨB) in weeks 1 and 2, but no fish using this route were detected downstream (σC = 

0.00) in either week. Such heterogeneity in survival and distribution among only three major 

migration routes reiterates the need to obtain a population-level understanding of distribution 

and survival through this spatially complex and hydraulically dynamic system. 

Comparisons of reach-specific estimates (appendix A, table A2) reveal that differences 

in fish-tag survival between routes A and C (highest and lowest fish-tag survival) can be 

attributed to the reaches represented by the parameters σa6 and σc1 (see fig. 2). These estimates 

indicate that 44 and 50 percent (weeks 1 and 2) of all tagged fish that arrived at the Turner CutSan Joaquin River junction and proceeded through the San Joaquin River, survived with a 

functioning tag (σa6) to another monitoring site (for example, Jersey Point, Three-Mile Slough, 

or the pumping facilities). In contrast, 0 and 3 percent (weeks 1 and 2) of the tagged fish that 

entered Turner Cut at this junction survived with a functioning tag (σc1) to another monitoring 

site. These findings indicate that fish entering Turner Cut either died or were delayed (relative to 

Route A) to the extent that their tags failed before exiting the Delta. 

20
A similar comparison of reach-specific estimates between routes A and B (San Joaquin 

River and Old River) reveals that the difference in fish-tag survival between these routes are 

probably not attributable to the reaches represented by parameters σa6 and σb1. Despite lower 

fish-tag survival in Route B compared to Route A, and although σb1 represents fish-tag survival 

over a greater distance (for example, analogous to σa3σa4σa5σa6 for Route A), 51–65 percent 

(between weeks) of tagged fish that entered Old River survived with a functioning tag (σb1) to 

another site. Rather, the data show that low fish-tag survival through the Clifton Court Forebay 

(σb2; appendix A, table A2) and between the intake at each of the pumping facilities and Chipps 

Island (σb3 and σd1) account for lower fish-tag survival through Old River compared to the San 

Joaquin River. Of all tagged fish that arrived at Clifton Court Forebay, we estimated that 37 and 

39 percent (weeks 1 and 2) survived with a functioning tag to the intakes of the State Water 

Project. Of those fish that arrived at the intakes of the State Water Project, we estimated that 16 

and 47 percent (weeks 1 and 2) exited the Delta with a functioning tag. Of those fish that arrived 

at the Central Valley Project, we estimated that 5 and 11 percent (weeks 1 and 2) exited the 

Delta with a functioning tag. In comparison, we estimated that 61 and 71 percent (weeks 1 and 

2) of fish that reached Jersey Point exited the Delta with a functioning tag (σa7). Although 

confidence intervals around these estimates are large (see appendix A, table A2), these results 

suggest that successful passage through the Delta through Old River is most limited by low 

survival or delays in reaches containing the Clifton Court Forebay, State Water Project, and 

Central Valley Project. 

Migration through the Central Delta 

“Successful” migration (defined as σr > 0) was observed in only two of the three 

pathways that were monitored. No tagged fish that entered Turner Cut were detected at Chipps 

Island. Salvage at the pumping facilities and subsequent transport also seemed to be the only 

successful migration pathway for tagged fish that traveled through Old River. The opposite was 

true of fish that traveled through the San Joaquin River past Turner Cut—successful migrants 

exclusively traveled past Jersey Point or Threemile Slough, rather than through the pumping 

projects. Detections at the three monitoring sites (MID, OSJ, FAL) that were excluded from the 

release-recapture model also support these observations. Of all tagged fish detected in Old 

River, only 2 percent were detected at any of these three sites, and one-half of those fish were 

detected at site FAL after salvage at the Central Valley Project, transport, and release into the 

western Delta. 

Fish that traveled through Old River also reached Chipps Island faster than fish that 

traveled through the San Joaquin River (fig. 4), although travel times were only available for 

fish that survived this reach and were detected at Chipps Island. Fish may have traveled faster 

through Old River because unlike fish that traveled through other routes, they experienced no 

reversing flows prior to salvage, transport, and release into the western Delta. 

21
Of all tagged fish detected in Turner Cut, only 4 percent were detected at any of the three 

sites that were not included in the release-recapture model. Although detection probabilities 

were not estimable at any of the three sites excluded from the model, 21 percent (40 of 186) of 

tagged fish known to use Route A were detected in these channels (sites MID, OSJ, FAL), but 

only one of these was detected at the Clifton Court Forebay or either pumping project. These 

results, along with the very low apparent success of migrants that traveled through Turner Cut 

(σc1 ≤ 0.03) provide evidence that conditions in the central Delta impose either mortality or long 

travel times (exceeding tag life of 2–20 days) on nearly all migrants that travel through the 

central Delta. 

Migration Past the Stockton Wastewater Treatment Plant 

In 2007, the San Joaquin River Group Authority (2009) observed that 116 of 776 tags 

released in the San Joaquin River were found “not moving” near the Stockton Wastewater 

Treatment Plant. Based on these observations, it was suspected that high mortality in this region 

might have been caused by degraded water quality from treatment plant effluent. In this study, 

fish-tag survival probabilities were relatively high (ranged 0.89 to 0.96 between weeks) through 

the reach containing the treatment plant. Based on our point estimates of fish-tag survival, we 

predict that about 8 of the 565 fish that were released upstream of the treatment plant and 

remained in the San Joaquin River past its junction with Old River, would have died in this 

reach. Because of the large difference between years, it seems reasonable to assume that 

mortality in this reach was lower in 2008 than in 2007. 

As a result of the suspected high mortality that was identified during the 2007 study, the 

San Joaquin River Group Authority (2009) monitored water quality and survival in this reach 

during 2008. Water-quality monitoring indicated that ammonia concentrations did not exceed 

U.S. Environmental Protection Agency standards during the study period. To evaluate fish 

survival, fish implanted with non-functioning tags were held in the river near the effluent of the 

wastewater treatment plant, but no mortalities or sub-lethal effects were observed. 

Summary 

Perry and others (in press) illustrated the importance of estimating both route 

entrainment and survival probabilities in order to gain an understanding of population-level 

survival during juvenile salmon migration through a complex system like the Delta. Compared 

to traditional mark-recapture techniques (for example, releases of coded wire tagged fish) 

acoustic telemetry provides greater temporal and spatial detail about the outmigration process. 

Further, continuous, simultaneous monitoring at several locations allows estimation of 

entrainment probabilities at river junctions and reach- and route-specific survival throughout the 

study region. If premature tag failure can be reduced to a negligible rate, future studies that use 

telemetry techniques should be able to address many important management questions, 

including the objectives of the VAMP. The rates of premature failure observed in this study 

were not observed in other studies using similar tags from the same manufacturer (Adams and 

others, 2008; Adams and Counihan, 2009) and were thus unexpected. In response to these 

results, the manufacturer has discontinued the tag model used in this study (795-S) and has redesigned their products to minimize the occurrence of premature tag failure in future studies (B. 

Ransom, HTI, oral commun., 2008 ). 

22
Although the joint fish-tag survival probabilities reported in this study may be of limited 

use to fishery and water resource managers, these data suggest that either high mortality or long 

travel times (relative to other routes) are prevalent among juvenile salmon migrating through the 

central Delta. Further, these results support the hypothesis that in the absence of a barrier at the 

head of Old River, the proportion of juvenile salmon traveling through Old River is similar to 

the fraction of San Joaquin River discharge flowing into Old River. There remains great 

potential to further understand the relations among discharge, water exports, and survival of 

migrating salmon through the San Joaquin River and Sacramento-San Joaquin Delta. Although 

complete answers to these questions will require replication over several years and a variety of 

conditions (for example, barrier placements, discharge, export operations), results from this 

study illustrate that these objectives are attainable. Recent advancements in acoustic telemetry 

technology, along with quantitative analytical approaches, should soon provide managers with 

much-needed data for salmon and water management in this system. 

Acknowledgments 

This work was funded under Interagency Agreement no. 08AA200078 with the U. S. 

Bureau of Reclamation with financial support provided by the U.S. Bureau of Reclamation, U.S. 

Fish and Wildlife Service, California Department of Water Resources, California Department of 

Fish and Game, San Joaquin River Group Authority, State Water Contractors and the San Luis 

and Delta-Mendota Water Authority. We thank P. Brandes (U.S. Fish and Wildlife Service) for 

managing the study; T. Liedtke (USGS Columbia River Research Laboratory) and A. Fuller 

(FishBio Environmental) for fish tagging and release; Dave Vogel (Natural Resource Scientists, 

Inc.), Jon Burau and Aaron Blake (USGS California Water Science Center) for installing and 

operating acoustic receivers; and Jon Burau and John Beeman (USGS Columbia River Research 

Laboratory) for reviewing this report. We also thank S. Brewer, S. Foott, J. Ingram, J. Lewis, M. 

Marshall, K. Nichols, P. Hrodey, B. Powell, J. Speegle, R. Stone, J. Thompson, C. Vallee, P. 

Voong, and L. Wichman (U.S. Fish and Wildlife Service); M. Abiouli, K. Clark, J. Miranda, A. 

Mueller, (California Department of Water Resources); C. Dale and D. Rocheleau (Natural 

Resource Scientists, Inc.); M. Archer (MBK Engineers); T. Ford and W. Monier (Modesto and 

Turlock Irrigation Districts); T. Stephens (Merced Irrigation District); S. Boyd (East Bay 

Municipal Utility District); E. Fuller, J. Inman, J. Pombo, and C. Sonke (FishBio 

Environmental); F. Bajjaliya, T. Devoe, C. Hanson, J. Karkanen, K. Karkanen, T. Musco 

(Hanson Environmental, Inc.); I. Werner (UC Davis); B. Herbold (U.S. Environmental 

Protection Agency;) L. Ploss and D. Westcot (San Joaquin River Group Authority); B. Bridges, 

L. Kiteck, S. Moore, and B. Wu (U.S. Bureau of Reclamation); J. Stuart (NOAA National 

Marine Fisheries Service); B. Anderson, M. Cozart, D. Gates, T. Heyne, S. Hoover, G. 

Litynksy, S. McCulloch, M. Serr, C. Sinclair, B. Smith, D. Thatcher, S. Tsao, L. Yamaguchi 

(California Department of Fish and Game); S. Borglin, R. Burks, J. Graham, J. Hanlon, K. 

Nyugen, C. Spier, and W. Stringfellow (University of Pacific); C. Battenfeld, J. George, T. 

Guerrero, and P. Stumpner, (USGS California Water Science Center); S. Brewer, J. Charrier, L. 

Gee, A. Grote, J. Plumb, M. Sholtis, and N. Swyers (USGS Columbia River Research 

Laboratory). 

23
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26
Appendix A. Parameter definitions and estimates 

Table A1. Definitions of parameters in the release-recapture model.

Parameter Definition 

S a0,DF Tag survival probability between implantation and release at Durham Ferry 

S a0,ST Tag survival probability between implantation and release at Stockton 

σa1 Combined probability of fish survival and tag survival from release at Durham Ferry to SJO(s) 

σa2 Joint probability of fish survival and tag survival from SJO.s to SJO(n),OLD 

σa3 Joint probability of fish survival and tag survival from SJO.n to STP.s 

σa4 Joint probability of fish survival and tag survival from STP.s to STP.n 

σa5,DF Joint probability of fish survival and tag survival from STP.n to SJT, TRN 

σa5,ST Joint probability of fish survival and tag survival from release at Stockton to SJT, TRN 

σa6 Joint probability of fish survival and tag survival from SJT to any of the next monitoring sites at 

TMS, JPT, CCFB, or CVP 

σa7 Joint probability of fish survival and tag survival from JPT to MAL 

σb1 Joint probability of fish survival and tag survival from OLD to any of the next monitoring sites at 

TMS, JPT, CCFB, or CVP 

σb2 Joint probability of fish survival and tag survival from CCFB to SWP 

σb3 Joint probability of fish survival and tag survival from SWP to MAL 

σc1 Joint probability of fish survival and tag survival from TRN to any of the next monitoring sites at 

TMS, JPT, CCFB, or CVP 

σd1 Joint probability of fish survival and tag survival from CVP to MAL 

σe1 Joint probability of fish survival and tag survival from TMS to MAL 

Ψa1 Probability of remaining in the San Joaquin River (i.e., passing site SJO.n) at the Old River-San 

Joaquin River junction; equivalent to (1 – Ψb1) 

Ψb1 Probability of moving from the San Joaquin River into Old River (i.e., passing site OLD) at the 

Old River-San Joaquin River junction; equivalent to (1 – Ψa1) 

Ψa2 Probability of remaining in the San Joaquin River (i.e., passing SJT) at the Turner Cut-San 

Joaquin River junction; equivalent to (1 – Ψc2) 

Ψc2 Probability of moving from the San Joaquin River into Turner Cut (i.e., passing TRN) at the 

Turner Cut-San Joaquin River junction; equivalent to (1 – Ψa2) 

φa6,a7 Probability of moving from SJT toward JPT and surviving from SJT to JPT 

φa6,b2 Probability of moving from SJT toward CCFB and surviving from SJT to CCFB 

φa6,d1 Probability of moving from SJT toward CVP and surviving from SJT to CVP 

φa6,e1 Probability of moving from SJT toward TMS and surviving from SJT to TMS 

φb1,a7 Probability of moving from OLD toward JPT and surviving from OLD to JPT 

φb1,b2 Probability of moving from OLD toward CCFB and surviving from OLD to CCFB 

φb1,d1 Probability of moving from OLD toward CVP and surviving from OLD to CVP 

φb1,e1 Probability of moving from OLD toward TMS and surviving from OLD to TMS 

φc1,a7 Probability of moving from TRN toward JPT and surviving from TRN to JPT 

φc1,b2 Probability of moving from TRN toward CCFB and surviving from TRN to CCFB 

φc1,d1 Probability of moving from TRN toward CVP and surviving from TRN to CVP 

φc1,e1 Probability of moving from TRN toward TMS and surviving from TRN to TMS 

Pa1,DF Detection probability in holding tanks at Merced River Hatchery during the 1 hr prior to 

departure from hatchery for fish released at Durham Ferry 

Pa1,ST Detection probability in holding tanks at Merced River Hatchery during the 1 hr prior to 

departure from hatchery for fish released at Stockton 

Pa2 Detection probability at SJO.s 

Pa3 Detection probability at SJO.n 

Pa4 Detection probability at STP.s 

Pa5 Detection probability at STP.n 

27
Table A1. Continued. 

Parameter Definition 

Pa6 Detection probability at SJT 

Pa7,DF Detection probability at JPT for fish released at Durham Ferry 

Pa7,ST Detection probability at JPT for fish released at Stockton 

Pa8,DF Detection probability at MAL for fish released at Durham Ferry 

Pa8,ST Detection probability at MAL for fish released at Stockton 

Pb1 Detection probability at OLD 

Pb2,DF Detection probability at CCFB for fish released at Durham Ferry 

Pb2,ST Detection probability at CCFB for fish released at Stockton 

Pb3 Detection probability at SWP 

Pc1 Detection probability at TRN 

Pd1 Detection probability at CVP 

Pe1 Detection probability at TMS 

Table A2. Parameter estimates (standard error in parentheses) with 95-percent profile likelihood 

confidence intervals (C.I.) for tagged juvenile Chinook salmon released during weeks 1 and 2. 

[Parameters without standard errors or confidence intervals were set to fixed values in the 

model] 

Week 1 Week 2 

Parameter 

Estimate 

(SE) 95% C. I. 

Estimate 

(SE) 95% C. I. 

S a0,DF 0.86 (0.02) 0.82, 0.90 0.92 (0.02) 0.88, 0.95 

S a0,ST 0.86 (0.03) 0.81, 0.91 0.95 (0.02) 0.91, 1.00 

σa1 0.92 (0.05) 0.82, 1.00 0.86 (0.02) 0.82, 0.90 

σa2 0.85 (0.07) 0.72, 0.99 0.96 (0.02) 0.92, 1.00 

σa3 0.85 (0.05) 0.75, 0.93 0.70 (0.05) 0.59, 0.79 

σa4 0.96 (0.03) 0.87, 0.99 0.89 (0.05) 0.78, 0.98 

σa5,DF 0.49 (0.07) 0.35, 0.63 0.56 (0.07) 0.42, 0.70 

σa5,ST 0.52 (0.04) 0.44, 0.60 0.64 (0.04) 0.56, 0.71 

σa6 0.51 (0.08) 0.37, 0.68 0.44 (0.05) 0.34, 0.54 

σa7 0.61 (0.11) 0.40, 0.81 0.71 (0.08) 0.55, 0.84 

σb1 0.62 (0.07) 0.51, 0.80 0.51 (0.05) 0.41, 0.62 

σb2 0.37 (0.09) 0.21, 0.56 0.39 (0.10) 0.21, 0.59 

σb3 0.16 (0.10) 0.03, 0.42 0.46 (0.15) 0.20, 0.75 

σc1 0.03 (0.03) 0.00, 0.12 0.00 

σd1 0.11 (0.05) 0.04, 0.22 0.05 (0.04) 0.01, 0.15 

σe1 0.52 (0.37) 0.04, 1.00 1.00 

Ψa1 0.32 (0.04) 0.25, 0.40 0.37 (0.03) 0.31, 0.44 

Ψb1 0.68 (0.04) 0.60, 0.75 0.63 (0.03) 0.56, 0.69 

Ψa2 0.68 (0.05) 0.58, 0.76 0.89 (0.03) 0.83, 0.94 

Ψc2 0.32 (0.05) 0.24, 0.42 0.11 (0.03) 0.06, 0.17 

φa6,a7 0.48 (0.08) 0.34, 0.65 0.40 (0.05) 0.31, 0.50 

φa6,b2 0.00 0.00 

φa6,d1 0.00 0.00 

φa6,e1 0.03 (0.02) 0.00, 0.08 0.04 (0.02) 0.01, 0.08 

φb1,a7 0.01 (0.01) 0.00, 0.04 0.01 (0.01) 0.00, 0.03 

φb1,b2 0.27 (0.06) 0.18, 0.41 0.21 (0.04) 0.14, 0.32 

φb1,d1 0.37 (0.05) 0.27, 0.47 0.29 (0.04) 0.22, 0.37 

φb1,e1 0.00 0.00 

φc1,a7 0.00 0.00 

28
Table A2. Continued. 

Week 1 Week 2 

Parameter 

Estimate 

(SE) 95% C. I. 

Estimate 

(SE) 95% C. I. 

φc1,b2 0.00 0.00 

φc1,d1 0.03 (0.03) 0.00, 0.12 0.00 

φc1,e1 0.00 0.00 

Pa1,DF 1.00 1.00 

Pa1,ST 1.00 1.00 

Pa2 0.36 (0.04) 0.29, 0.44 0.99 (0.01) 0.96, 1.00 

Pa3 0.98 (0.02) 0.92, 1.00 0.98 (0.02) 0.92, 1.00 

Pa4 0.92 (0.04) 0.82, 1.00 1.00 

Pa5 1.00 0.96 (0.04) 0.85, 1.00 

Pa6 1.00 1.00 

Pa7,DF 0.67 (0.10) 0.45, 0.84 1.00 

Pa7,ST Pa7,DF 0.77 (0.08) 0.59, 0.90 

Pa8,DF 0.96 (0.03) 0.88, 1.00 0.98 (0.02) 0.91, 1.00 

Pa8,ST Pa8,DF 0.98 (0.02) 0.91, 1.00 

Pb1 0.47 (0.06) 0.37, 0.58 0.94 (0.03) 0.86, 0.98 

Pb2,DF 0.77 (0.12) 0.50, 0.94 0.82 (0.12) 0.54, 0.97 

Pb2,ST Pb2,DF 0.00 

Pb3 1.00 1.00 

Pc1 1.00 1.00 

Pd1 1.00 1.00 

Pe1 1.00 1.00 

29
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Holbrook and others—Distribution and Joint Fish-Tag Survival of Juvenile Chinook Salmon Migrating through the Sacramento-San Joaquin River Delta, California, 2008—Open-File Report 2009-1204