Prepared in cooperation with the U.S. Fish and Wildlife Service

Survival and Migration Route Probabilities of Juvenile 

Chinook Salmon in the Sacramento-San Joaquin River 

Delta During the Winter of 2009–10

U.S. Department of the Interior

U.S. Geological Survey

Open-File Report 2012–1200
Cover: Image Courtesy of NASA.
Survival and Migration Route Probabilities of Juvenile 

Chinook Salmon in the Sacramento-San Joaquin River 

Delta during the Winter of 2009–10

By Russell W. Perry, Jason G. Romine, and Scott J. Brewer, U.S. Geological Survey; Peter E. LaCivita, 

William N. Brostoff, U.S. Army Corps of Engineers; and Eric D. Chapman, University of California at Davis

 

Prepared in cooperation with the 

U.S. Fish and Wildlife Service

Open-File Report 2012-1200

U.S. Department of the Interior

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

KEN SALAZAR, Secretary

U.S. Geological Survey

Marcia K. McNutt, Director

U.S. Geological Survey, Reston, Virginia: 2012

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Suggested citation:

Perry, R.W., Romine, J.G., Brewer, S.J., LaCivita, P.E., Brostoff, W.N., and Chapman, E.D., 2012, 

Survival and migration route probabilities of juvenile Chinook salmon in the Sacramento-San Joaquin 

River Delta during the winter of 2009–10: U.S. Geological Survey Open-File Report 2012-1200, 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.
iii

Contents

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

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

Methods........................................................................................................................................................... 5

Telemetry System........................................................................................................................................ 5

Fish Tagging and Release ........................................................................................................................... 7

Model Development ..................................................................................................................................... 8

Parameter Estimation ................................................................................................................................10

Survival through the Delta..........................................................................................................................12

Results...........................................................................................................................................................14

River Conditions and Migration Timing ......................................................................................................14

Detection Probabilities ...............................................................................................................................14

Route-Specific Survival through the Delta..................................................................................................16

Migration Routing.......................................................................................................................................21

Relative Contributions to SDelta ...................................................................................................................22

Discussion .....................................................................................................................................................23

Acknowledgments .........................................................................................................................................25

References Cited...........................................................................................................................................25

Appendix A ....................................................................................................................................................28

Figures

Figure 1. Maps of the Sacramento-San Joaquin River Delta with shaded regions showing river reaches 

that comprise survival through the Delta for four different migration routes................................................... 4

Figure 2. Map showing location of telemetry stations used to estimate survival and migration route 

probabilities within four major migration routes of the Sacramento-San Joaquin River Delta during the 

winter of 2009–10 .......................................................................................................................................... 6

Figure 3. Schematic of the mark-recapture model used to estimate survival (Shi), detection (Phi), route 

entrainment (Ψhl), and joint survival-entrainment (φhi,jk) probabilities of juvenile late-fall Chinook salmon 

migrating through the Sacramento–San Joaquin River Delta for releases made in winter of 2009–10 ......... 9

Figure 4. River discharge, water exports, and Delta Cross Channel discharge during the migration period 

of tagged juvenile Chinook salmon migrating through the Sacramento-San Joaquin River Delta during 

winter of 2009–10 ........................................................................................................................................ 15

Figure 5. Probability of surviving migration through the Sacramento-San Joaquin River Delta (Sh) for 

each of four migration routes for tagged late-fall juvenile Chinook salmon migrating from the 

Sacramento River........................................................................................................................................ 18

Figure 6. Comparison of route-specific survival between the Sacramento River (A), Sutter Slough (B1), 

and Steamboat Slough (B2) for late-fall Chinook salmon tagged and released in December 2009 

(R1 and R2) and February 2010 (R3 and R4) ................................................................................................ 19

Figure 7. Cumulative survival for each migration route as a function of distance traveled for juvenile latefall Chinook salmon released in December 2009 (R1 and R2) and February 2010 (R3 and R4) ................... 20
iv

Tables

Table 1. Summary of release dates, locations, and sample size of acoustically tagged late-fall Chinook 

salmon released into the Delta during the winter of 2009–10 ........................................................................ 8

Table 2. Route-specific survival through the Sacramento–San Joaquin River Delta (Sh) and the probability 

of migrating through each route (Ψh) for acoustically tagged fall-run juvenile Chinook salmon released 

December 2–5, 2009 (R1) and December 16–19, 2009 (R2) ....................................................................... 17

Table 3. Ratio (θh) of survival through route h (Sh) to survival through the Sacramento River (SA) 

for acoustically tagged late fall-run juvenile Chinook salmon released in December 2–5 and 

December 16–19, 2009 ............................................................................................................................... 21

Table 4. Probability of migrating through each route (Ψh) for acoustically tagged late fall-run juvenile 

Chinook salmon released in December 2009 as a function of gate position when fish passed the Delta 

Cross Channel............................................................................................................................................. 22

Conversion Factors

Multiply By To obtain

Length

foot (ft) 0.3048 meter (m)

mile (mi) 1.609 kilometer (km)

Area

square foot (ft2) 0.09290 square meter (m2)

Volume

cubic foot (ft3) 0.02832 cubic meter (m3) 

Flow rate

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

Temperature in degrees Celsius (°C) may be converted to degrees Fahrenheit (°F) as follows:°F=(1.8×°C)+32. 

Temperature in degrees Fahrenheit (°F) may be converted to degrees Celsius (°C) as follows:°C=(°F-32)/1.8
1

Survival and Migration Route Probabilities of Juvenile 

Chinook Salmon in the Sacramento-San Joaquin River 

Delta during the Winter of 2009–10

By Russell W. Perry, Jason G. Romine, and Scott J. Brewer, U.S. Geological Survey; Peter E. LaCivita, 

William N. Brostoff, U.S. Army Corps of Engineers; and Eric D. Chapman, University of California at Davis

Abstract

Juvenile Chinook salmon (Oncorhynchus tshawytscha) emigrating from natal tributaries 

of the Sacramento River may use a number of migration routes to negotiate the Sacramento-San 

Joaquin River Delta (hereafter, “the Delta”), each of which may influence their probability of 

surviving. We applied a mark-recapture model to data from acoustically tagged juvenile late-fall 

Chinook salmon that migrated through the Delta during the winter of 2009–10 (hereafter, 2010). 

This report presents findings from our fourth year of research. 

We estimated route-specific survival for four release groups: two release groups that 

migrated through the Delta in December 2009 and January 2010, and two release groups that 

migrated during February 2010. Population-level survival through the Delta (SDelta) ranged from 

0.374 (SE = 0.040) to 0.524 (SE = 0.034) among releases. Although river flows for the February 

release groups were substantially higher (20,000–40,000 ft3/s at Freeport) than for the December 

release groups (about 10,000 ft3/s), SDelta did not differ considerably between release groups. 

Among migration routes, fish migrating through the Sacramento River exhibited the highest 

survival, and fish entering the interior Delta exhibited the lowest survival. Fish entering Sutter 

and Steamboat Sloughs had lower survival than fish entering the Sacramento River during 

December, but similar survival during February. These patterns were consistent among release 

groups, and strikingly similar to patterns observed in previous years. 

Migration routing varied among release groups partly because of differences in river 

discharge between releases. For the two December release groups, 26.5 and 28.9 percent of fish 

entered the interior Delta; for the two February release groups, 10.4 and 17.9 percent of fish 

entered the interior Delta. Differences in routing probabilities between December and February 

are partly related to the inverse relationship between flow and the fraction of discharge entering 

the interior Delta. The proportion of fish diverted into the interior Delta also can be affected by 

the status of the Delta Cross Channel’s gates. The fraction of fish entering Sutter and Steamboat 

Sloughs also varied considerably among release groups from 22.1 to 44.7 percent, and did not 

appear correlated to river discharge. For example, the lowest and highest proportion of fish 

entering Sutter and Steamboat Sloughs occurred during February. Because fish entering Sutter 

and Steamboat Sloughs bypass the entrance to the interior Delta, a high proportion of fish 

migrating into this route reduces the proportion of fish entering the interior Delta.
2

Introduction

Many stocks of Chinook salmon (Oncorhynchus tshawytscha) in California, Washington, 

and Oregon are listed as threatened or endangered under the Endangered Species Act (Nehlsen 

and others, 1991; Myers and others, 1998). In the Central Valley of California, the winter, 

spring, and fall/late fall runs of Chinook salmon are federally listed as endangered, threatened, 

and “species of concern,” respectively (National Marine Fisheries Service, 1997). Recently, due 

to below-target returns of fall Chinook salmon to the Sacramento River, the National Marine 

Fisheries Service declared a Federal Disaster and closed the 2008 salmon fishery along the West 

Coast (National Oceanic and Atmospheric Administration, 2008). Understanding factors 

affecting survival of salmon is critical to developing effective recovery strategies for these 

populations. 

An important stage in the life history of Chinook salmon is the period of migration from 

natal tributaries to the ocean, when mortality of juvenile salmon in the Sacramento River may 

increase from a host of anthropogenic and natural factors (Baker and Morhardt, 2001; Brandes 

and McLain, 2001; Williams, 2006). Juvenile Chinook salmon emigrating from the Sacramento 

River must pass through the Sacramento-San Joaquin River Delta (hereafter, “the Delta”), a 

complex network of natural and man-made river channels linking the Sacramento River with San 

Francisco Bay (Nichols and others, 1986). Juvenile salmon may migrate through a number of 

routes on their journey to the ocean—for example, they may migrate within the mainstem 

Sacramento River leading directly into San Francisco Bay (see Route A in fig. 1). However, 

juvenile salmon also may migrate through longer secondary routes such as the interior Delta, the 

network of channels to the south of the mainstem Sacramento River (see Routes C and D in fig. 

1). Juvenile salmon entering the interior Delta also are exposed to entrainment at water pumping 

projects in the southern Delta, which may decrease survival of fish using this migratory pathway 

(Kjelson and others, 1981; Brandes and McLain, 2001; Newman and Rice, 2002; Newman, 

2003; Kimmerer, 2008; Newman, 2008; Newman and Brandes, 2010). 

There is limited understanding of how water management actions in the Delta affect the 

population distribution and the route-specific survival of juvenile salmon. To address these 

uncertainties, we developed a mark-recapture model to estimate the route-specific components of 

population-level survival for acoustically tagged, late-fall Chinook smolts migrating through the 

Delta (Perry and others, 2010). This study provided the first quantitative estimates of routespecific survival through the Delta, and of the fraction of the population that uses each migration 

route. Furthermore, we explicitly quantified the relative contribution of each migration route to 

population-level survival. As with other authors (Newman and Brandes, 2010), we found that 

survival of fish migrating through the interior Delta was lower than survival of fish migrating 

through the Sacramento River. The proportion of the population entering the interior Delta 

differed between releases, which can influence population-level survival by shifting a fraction of 

the population from a low-survival migration route (the interior Delta) to a high-survival route 

(the Sacramento River). However, differences between releases in population-level survival were 

caused by changes in survival for given migration routes. These findings indicated that variation 

in population-level survival was driven both by variation in movement among routes and 

survival within routes. 
3

In this report, we estimate survival and migration route probabilities for acoustically 

tagged late-fall Chinook salmon migrating through the Delta during the winter of 2009–10 

(hereafter, 2010). This report presents survival estimates of the study’s fourth consecutive year, 

providing important insights into interannual variations in route-specific survival and movement 

through the Delta. Design aspects of our previous study were maintained, but some aspects 

differed from previous years. The primary difference in study design between 2010 and previous 

years is the number of release groups, release timing, and release locations. Two releases were 

conducted in migration years 2007–09—one in December when the Delta Cross Channel was 

open, and one in January when the Delta Cross Channel was closed. An additional group of fish 

also was released into Georgiana Slough in 2008 and 2009 to increase sample sizes of fish 

migrating through the interior Delta. In comparison, for the 2010 migration year, two releases 

were conducted in December 2009, each consisting of two release locations (40 km upstream of 

Freeport at the Elkhorn boat ramp in the Sacramento River and in Georgiana Slough). The 

release at the Elkhorn Boat Ramp was farther upstream than the releases made near Sacramento 

in previous years. The release in early December was conducted when the Delta Cross Channel 

was open, and the later release in December was conducted when the Delta Cross Channel was 

closed. In addition, tagged fish released in December were only held for a minimum of 11–12 

hours prior to release, whereas in previous years fish were held for a minimum of 24 hours prior 

to being released over a 24-hour period. We also estimated survival for two additional releases in 

February 2010 conducted by the U.S. Army Corps of Engineers. These groups were released at 

the Elkhorn Boat ramp in the Sacramento River upstream of the Delta. 
4

Figure 1. Maps of the Sacramento-San Joaquin River Delta with shaded regions showing river reaches 

that comprise survival through the Delta for four different migration routes. For routes C and D, the interior 

Delta is the large shaded region in the southernmost section of the migration route. 
5

Methods

Telemetry System

Telemetry stations were deployed to monitor movement of tagged fish among four major 

migration routes through the Delta (fig. 1)—the mainstem Sacramento River (Route A), 

Steamboat and Sutter Sloughs (Route B), the interior Delta through the Delta Cross Channel 

(Route C), and the interior Delta through Georgiana Slough (Route D; fig. 1). Telemetry stations 

were labeled hierarchically to reflect the branching nature of channels at river junctions and their 

subsequent downstream convergence at the confluence of river channels (fig. 2). Each telemetry 

station consisted of single or multiple receivers (Vemco Ltd., Model VR2) that identified 

individual fish based on the unique pattern of acoustic pulses emitted from a transmitter. Because 

the Sacramento River is the primary migration route, the ith telemetry station within this route 

was denoted as Ai from the release site to the last telemetry station in the Delta at Chipps Island 

(A9). Sutter and Steamboat Sloughs (labeled Bi) diverge from the Sacramento River at the first 

river junction and converge again with the Sacramento River upstream of A7. We deployed 

numerous telemetry stations within Sutter and Steamboat Sloughs to quantify survival and 

movement within this region. Specifically, Sutter and Miner Sloughs form a northern route, and 

stations along this route are labeled B11 (entrance to Sutter Slough), B12, and B13 (Miner Slough; 

fig. 2). A southern route is formed by Steamboat Slough, and these stations were labeled as B21, 

B22, and B23. The entrance to the interior Delta through the Delta Cross Channel was labeled as 

C1 where it diverges from the Sacramento River at the second river junction. Telemetry stations 

within Georgiana Slough and the interior Delta were labeled as Di beginning where Georgiana 

Slough diverges from the mainstem Sacramento River at the second river junction (D1) until the 

convergence of the interior Delta with the Sacramento River at D7. Following this hierarchy, 

routes A, B, C, and D contained 8, 6, 1, and 7 telemetry stations. In addition, to quantify 

movement between the lower Sacramento River and the lower San Joaquin River, we included a 

telemetry station within Three Mile Slough (E1) for a total of 23 telemetry stations within the 

Delta. Parameter subscripting and coding of detection histories followed this hierarchical 

structure (see section, “Model Development”). 
6

Figure 2. Map showing location of telemetry stations used to estimate survival and migration route 

probabilities within four major migration routes of the Sacramento-San Joaquin River Delta during the 

winter of 2009–10. Red-filled circles labeled as hi show the location of telemetry station i with route h. 

Locations denoted by unfilled circles show telemetry stations used in 2007–08 but not 2009–10. Station A10

pools all telemetry stations in San Francisco Bay downstream of A9. The Elkhorn Boat Ramp release site 

was 40 river kilometers upriver of station A2, and the Georgiana release site is noted as the yellow-filled 

circle labeled as RGeo. 
7

With this configuration of telemetry stations, survival in the final reach (downstream of 

A8 and D7) is confounded with detection probability at the last telemetry station (Skalski and 

others, 2001). Therefore, to estimate survival to the terminus of the Delta, and detection 

probability at the last station in the Delta (A9), we formed one additional telemetry station by 

pooling detections from numerous stations downstream of A9 in San Francisco Bay (fig. 2). Most 

of these detections occurred at bridge-mounted telemetry stations that provided nearly complete 

cross-sectional coverage of San Francisco Bay, but single-monitor stations at other locations also 

were included. 

Fish Tagging and Release

Juvenile late-fall Chinook salmon were obtained from the Coleman National Fish 

Hatchery (about 340 river kilometers upstream of the Elkhorn Boat Ramp near Sacramento). 

Fish were surgically implanted with a 1.6-g tag with a 70-d expected battery life (Vemco Ltd., 

Model V7-2L-R64K). Four releases were made at the Elkhorn Boat ramp, two in December 2009 

(R1 and R2), one in January 2010 (R3), and one in February 2010 (R4). Hereafter, R1 and R2 are 

referred to as the December release groups, while R3 and R4 are referred to as the February 

release groups. The December releases were done on behalf of the U.S. Fish and Wildlife 

Service (USFWS), and the February releases were done on behalf of the U.S. Army Corps of 

Engineers (USACE; table 1). 

For the December release groups, tags had a pulse delay of 20–60 s. Except for a 

minimum size criteria of 140-mm fork length, fish were randomly selected for tagging, resulting 

in a mean fork length (FL) of 153.3 mm (SD = 10.35) and mean weight of 41.1 g (SD = 9.4) for 

December releases. Fish were fasted for 24 h prior to surgery to ensure a post-absorptive state.

To surgically implant transmitters, fish were anaesthetized using tricaine methanesulphonate 

(MS222). Once anesthetized, a small incision was made in the abdomen between the pectoral 

fins and the pelvic girdle. The transmitter was inserted into the peritoneal cavity, and the incision 

was closed with two interrupted sutures (4-0 nylon sutures with FS-2 cutting needle). After 

tagging was complete, fish were held for 24 hours before being transported to release sites at

either the Sacramento River at Elkhorn Boat Ramp (40 km upstream of the Freeport station at 

A2) or Georgiana Slough (about 5 km downstream of D1; fig. 2). Tagged fish were then 

transferred to perforated 19-L buckets (two fish per bucket), held for 11–12 h at the release site 

to allow recovery from the transportation process, and then released every 4 hours at Sacramento 

and every 2 hours at Georgiana Slough. Each group was released over a 24-hour period to 

distribute release times over the tidal and diel cycle (table 1). Fish were released into Georgiana 

Slough 2 days after the Elkhorn release group to correlate release times in Georgiana Slough 

with the travel time of fish from Elkhorn Boat Ramp to Georgiana Slough. 

For the February release groups, tags had a random pulse delay of 15–45 seconds. The 

tagged fish used for this release were obtained from the Coleman National Fish Hatchery and 

transported to University of California, Davis, where they were held prior to tagging. Fish used 

for this release had a mean fork length of 177.2 mm (SD=13.7) and a mean weight of 66.8 g 

(SD=29.4). Tagging procedures followed the same protocol as previously mentioned. Tagging 

was conducted over a 2-week period prior to release. Fish were then transported to Elkhorn Boat 

Ramp for release. Upon arrival at the release site, the river temperature was taken to ensure the 

fish were not stressed by a large temperature fluctuation, and the water was tempered 

accordingly. All fish were then released into the river after dark in order to provide refuge from 

predators within the first few hours of release. 
8

Table 1. Summary of release dates, locations, and sample size of acoustically tagged late-fall Chinook 

salmon released into the Delta during the winter of 2009–10. 

[Agency: USACE, U.S. Army Corps of Engineers; USFWS, U.S. Fish and Wildlife Service] 

Agency Release date Release No. Release location Sample size

USFWS December 2–3, 2009 1 Sacramento 167

USFWS December 5, 2009 1 Georgiana Slough 72

USFWS December 16–17, 2009 2 Sacramento 168

USFWS December 19, 2009 2 Georgiana Slough 72

USACE January 30, 2010 3 Sacramento 249

USACE February 5, 2010 4 Sacramento 248

Model Development 

We used the same survival model as the one developed for the 2008–09 migration year, 

presented in Perry and Skalski (2010). In this model, we estimated detection (Phi), survival (Shi), 

route entrainment probabilities (Ψhl), and joint survival-entrainment probabilities (φhi,jk).

Detection probabilities (Phi) estimate the probability of detecting a transmitter assuming a fish is 

alive and the transmitter operational at telemetry station i within route h (h = A, B, C, D; fig. 2). 

Survival probabilities (Shi) estimate the probability of surviving from telemetry station i to i+1 

within route h (that is, to the next downstream telemetry station), conditional on surviving to 

station i (figs. 2 and 3). Route entrainment probabilities (Ψhl) estimate the probability of a fish 

entering route h at junction l (l = 1, 2), conditional on fish migrating through junction l (figs. 2 

and 3). Joint survival-entrainment probabilities (φhi,jk) estimate the joint probability of surviving 

from site hi to jk and moving into route j. The φhi,jk parameters are estimated in reaches with river 

junctions that split into two channels, but where telemetry stations within each river channel are 

located some distance downstream of the river junction. For example, fish passing station A7 in 

the Sacramento River may enter Three Mile Slough (E1) or remain in the Sacramento River for 

another 5.5 km downstream of this junction to pass station A8 (fig. 2). Thus, φhi,jk is the joint 

probability of surviving from A7 to its junction with Three Mile Slough, remaining in the 

Sacramento River at this junction, and then surviving from the junction to A8. 

For this study, telemetry stations within Sutter and Steamboat Sloughs downstream of 

each entrance allowed us to estimate route entrainment probabilities separately for each slough 

(figs. 2 and 3). The parameter ΨB11 estimates the probability of being entrained into Sutter 

Slough at station B11, and ΨB21 estimates the probability of being entrained into Steamboat 

Slough at station B21. Because route entrainment probabilities must sum to one at a given river 

junction, 1-ΨB11-ΨB21 = ΨA1 is the probability of remaining in the Sacramento River at the first 

junction (figs. 2 and 3).

As in previous years, the second junction was modeled as a three-branch junction where

ΨA2, ΨC2, and 1-ΨA2-ΨC2 = ΨD2 estimate the probabilities of remaining in the Sacramento River 

(Route A), being entrained into the Delta Cross Channel (Route C), and entering Georgiana 

Slough (Route D) at junction 2 (figs. 2 and 3). However, a substantial fraction of the first release 

group passed the Delta Cross Channel after the gates had closed. Therefore, as with migration 

years 2007 and 2009 (Perry and others, 2010; Perry and Skalski, 2010), we incorporated a 
9

Figure 3. Schematic of the mark-recapture model used to estimate survival (Shi), detection (Phi), route

entrainment (Ψhl), and joint survival-entrainment (φhi,jk) probabilities of juvenile late-fall Chinook salmon 

migrating through the Sacramento–San Joaquin River Delta for releases made in winter of 2009–10. The 

parameter ωn is the probability of passing the second river junction when the Delta Cross Channel was 

either open or closed. Release sites are denoted by Rm (m = Sac (Sacramento) and Geo (Georgiana 

Slough)), parameters subscripted by n are conditional on the position of the Delta Cross Channel gate, and 

m denote parameters which can be estimated separately for each release site.

PA2

PB21 PA3 PB11

PB12

PB13

PB22

PB23

PA4

PA8, m

PA7

PA9, m

PD7, m

PD4, m

PD2, m

PD1 PC1

RGeo

RSac

PE1, m

SA1

SA2

SA3

SD1,Geo, n

SD1,Sac, n SC1

SB13

SB12 SB22

SA4, n

SB23

SA8, m

SE1,A8,m SE1,D7,m

SD7, m

φ D4,D7,m

φ A7,E1 φ D4,E1, m

φ A7,A8

SD2, m

λ m

φ B11,B12

φ B11,B22

ΨB11 ΨB21 ΨA1

ω n ΨA2,n

ω n ΨD2,m

ωnΨC2,m

Junction 1

Junction 2

φ B11,B12

φ B11,B22
10

parameter to estimate the probability of fish passing this river junction when the gates were open 

(ωopen, fig. 3). We then estimated route entrainment probabilities conditional on gate position 

(i.e., Ψhl,open and Ψhl,closed). Route-specific survival was estimated for each release group. For the 

first release group, route-specific survival represents the average survival over conditions 

experienced by this release-group; that is, with the Delta Cross Channel gates both open and 

closed.

Joint survival-entrainment probabilities were estimated for three reaches where (1) fish 

entering Sutter Slough (B11) or Steamboat Slough (B21) may subsequently continue down either 

Miner Slough (B12) or Steamboat Slough (B22), (2) fish entering the San Joaquin River at D4 may 

subsequently exit this reach through either Three Mile Slough at E1 or the San Joaquin River at 

D7, and (3) fish passing A7 in the Sacramento River may exit this reach at either E1 or A8 (figs. 2 

and 3). Each of these reaches consist of a single river channel, a junction where the channel 

splits, and then two separate channels through which fish migrate before being detected at 

telemetry stations in each channel. In these locations, interest may lie in estimating the 

proportion of fish entering each channel (that is, the route entrainment probabilities, Ψhl).

However, when telemetry stations are located kilometers downstream of the river junction where 

fish enter one route or another, then estimates of Ψhl may be biased if survival probabilities 

downstream of the junction differ between the two channels. Despite this, estimates of the joint 

probability of surviving and migrating through a given channel (that is, φhi,jk) will remain 

unbiased in these circumstances. Although the φhi,jk parameters are difficult to interpret 

biologically, being the joint probability of entrainment and survival, their sum yields the total 

reach survival. Therefore, in the reaches where φhi,jk parameters are estimated, SB11 = φB11,B12 + 

φB11,B22, SB21 = φB21,B12 + φB21,B22, SA7 = φA7,E1 + φA7,A8, and SD4 = φD4,E1 + φD4,D5 are the 

probabilities of surviving from each upstream telemetry station to either of the next downstream 

stations. 

Parameter Estimation

Prior to parameter estimation, the records of tag detections were processed to eliminate 

false positive detections using methods based on Skalski and others (2002) and Pincock (2008). 

False positive detections of acoustic tags occur primarily when two or more tags are 

simultaneously present within the range of a given telemetry station, and simultaneous tag 

transmissions “collide” to produce a valid tag code that is not actually present at the monitor 

(Pincock, 2012). Our first criterion considered detections as valid if a minimum of two 

consecutive detections occurred within a 30-min period at a given telemetry station. Although 

this criterion minimized the probability of accepting a false positive detection, Pincock (2008) 

showed that a pair of false positive detections with a time interval less than 30 min occurred on 

average once every 30 days when simulating 10 tags simultaneously present at a monitor. Thus, 

our second criterion considered records with two detections at a given location as valid only if 

these detections were consistent with the spatiotemporal history of a tagged fish moving through 

the system of telemetry stations (Skalski and others, 2002). Detection records of fish that showed 

direct upstream movement over long distances against the flow were classified as predated fish.

The detection records for 6 percent of fish showed evidence of predation, and were truncated to 

the hypothesized last known location of the live tagged fish. All other detections were considered 

to be live juvenile salmon. In the lower Sacramento and San Joaquin Rivers (sites A7, A8, and 

D2), flows are tidally influenced, which can cause fish to move upstream during flood tides. To 
11

accommodate this behavior, the final downstream series of detections were used to form capture 

histories. 

Detection histories compactly describe the migration and detection process of fish 

moving through the network of telemetry stations. For example, a fish with the history 

AA0AAAAEDDDAA indicates it was released at Sacramento (“A”), detected in the Sacramento 

River at A2 (“A”), and not detected in the Sacramento River at A3 (“0”). This fish was 

subsequently detected at every other telemetry station as it migrated from the Sacramento River 

(“AAAA”) through Three Mile Slough (“E”), down the San Joaquin River (“DDD”), and finally 

past Chipps Island into San Francisco Bay (“AA”). Each detection history represents one cell of 

a multinomial distribution where the probability of each cell is defined as a function of the 

detection, survival, route entrainment, and joint survival-entrainment probabilities (see Perry and 

others, 2010, for an example). Given these 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 β π=∝∏  , (1) 

where Lkm is the likelihood for the kth release group (k = 1, ..., 4) at the mth release site [m = 

Sacramento (Sac), Georgiana Slough (Geo)], Rkm is the number of fish released for each release 

group and release site, njkm is the number of fish with the jth detection history in the kth release 

group at the mth release site, and πjkm is the probability of the jth detection history in the kth 

release group at the mth release site expressed as a function of the parameters ( β



). The 

likelihood was numerically maximized with respect to the parameters using algorithms provided 

in the software program USER (Lady and others, 2008). Parameters were estimated separately 

for each release (k) but simultaneously for both release sites by expressing the joint likelihood as 

the product of Lk,Sac and Lk,Geo. The variance-covariance matrix was estimated as the inverse of 

the Hessian matrix. We used the delta method (Seber, 1982) to estimate the variance of 

parameters that are functions of the maximum likelihood estimates. Uncertainty in parameter 

estimates is presented both as standard errors and 95-percent confidence intervals (that is, 

estimate ± 1.96*SE). 

For each release, the full model was considered as the model with the fewest parameter 

constraints, which still allowed all parameters to be uniquely estimated. When parameter 

estimates occur at the boundaries of one (or zero), they cannot be estimated through iterative 

maximum likelihood techniques and must be set to one (or zero). In our study, many detection 

probabilities were set to one because all fish passing a given location were known to have been 

detected at that location. In some cases, survival probabilities were fixed to one because all fish 

detected at a given telemetry station also were detected at the next downstream location. In 

addition, parameters for Route C (the Delta Cross Channel) were set to zero when the Delta 

Cross Channel was closed. A full detailing of parameter constraints applied under the full model 

is provided in appendix A. 

The purpose of including a separate release into Georgiana Slough was to improve 

precision of survival estimates within the interior Delta by increasing the sample size of fish 

migrating through this region. Pooling data across release sites can improve precision, but 

assumes that the fish released into the Sacramento River and Georgiana Slough experienced 

similar survival and detection probabilities in reaches through which both release groups 
12

migrated. Therefore, we used Akaike Information Criterion (AIC; Akaike, 1974) to evaluate 

hypotheses about equality in detection and survival parameters between release sites. For each 

release group, we compared the full model to a reduced model where all parameters were set 

equal between release sites. When AIC differed by greater than 2 between models, the model 

with lower AIC was selected as the most parsimonious model. We then used parameter estimates 

from the selected model for estimating population-level and route-specific survival through the 

Delta.

Survival through the Delta

Survival through the Delta is defined as the probability of survival from the entrance to 

the Delta at station A2 (Freeport) to the exit of the Delta at station A9 (Chipps Island).

Population-level survival through the Delta was estimated from the individual components as: 

D

Delta

A

h h

h

S S =

= Ψ ∑ , (2) 

where Sh is the probability of surviving the Delta given the specific migration route taken 

through the Delta, and Ψh is the probability of migrating through the Delta via one of four 

migration routes (A = Sacramento River, B = Steamboat and Sutter Sloughs, C = Delta Cross 

Channel, D = Georgiana Slough). Thus, population survival through the Delta is a weighted 

average of the route-specific survival probabilities with weights equal to the fraction of fish 

migrating through each route. 

Migration route probabilities are a function of the route entrainment probabilities at each 

of the two river junctions: 

ΨA = ΨA1ΨA2, (3)

ΨB = ΨB11 + ΨB21, (4) 

ΨC = ΨA1ΨC2, and (5)

ΨD = ΨA1ΨD2. (6)

 

For instance, consider a fish that migrates through the Delta via the Delta Cross Channel 

(Route C). To enter the Delta Cross Channel, this fish first remains in the Sacramento River at 

junction 1 with probability ΨA1, after which it enters the Delta Cross Channel at the second river 

junction with probability ΨC2. Thus, the probability of a fish migrating through the Delta through 

the Delta Cross Channel (ΨC) is the product of these route entrainment probabilities, ΨA1ΨC2. 

When population level survival can be broken down into components of routeentrainment probabilities and reach specific survival, then survival through the Delta for a given 

migration route (Sh) is simply the product of the reach-specific survival probabilities that trace 

each migration path through the Delta between the points A2 and A9 (see Perry and others, 2010).

However, when joint survival-entrainment probabilities are included in the model, survival 

through a given route must take into account all possible within-route pathways that involve the 

φhi,jk parameters. For example, survival through the Delta for fish that remain in the Sacramento 

River through the first and second river junctions is expressed as:

S SSS S S S A A2 A3 A4 A7,A8 A8 A7,E1 E1,D7 D7 = (φ φ+ ). (7) 
13

The bracketed term is the weighted average survival between A7 (Rio Vista) and A9

(Chipps Island) with the φhi,jk parameters weighting survival of fish that remain in the 

Sacramento River and survival of fish that finish their migration in the lower San Joaquin River 

after passing through Three Mile Slough. Thus, Delta survival for Route A (the Sacramento 

River) includes some mortality of fish that enter the interior Delta, and it is impossible to factor 

out this mortality without explicitly estimating route entrainment probabilities at the junction of 

the Sacramento River with Three Mile Slough. 

Survival through the Delta for fish taking the Delta Cross Channel (Route C) and 

Georgiana Slough (route D) is expressed similarly and explicitly accounts for fish that pass 

through Three Mile Slough and finish their migration in the lower Sacramento River: 

S SSS S S S C A2 A3 C1 D4,D7 D7 D4,E1 E1,A8 A8 = (φ φ+ ) , (8)

and S SSSS S S S D A2 A3 D1 D2 D4,D7 D7 D4,E1 E1,A8 A8 = (φ φ+ ) . (9) 

We pooled Sutter and Steamboat Sloughs into a single migration route, but survival 

through the Delta can be estimated separately for fish that enter Sutter Slough and fish that enter 

Steamboat Slough: 

B B11 B1 B21 B2 SS S =Ψ +Ψ , (10) 

where SB is survival through the Delta for fish that enter either Sutter or Steamboat Sloughs, SB1

and SB2 are survival through the Delta for fish that enter Sutter and Steamboat Sloughs, 

respectively, and where SB1 and SB2 are estimated as: 

S S SS SS S S S B1 A2 B11,B12 B12 B13 B11,B22 B22 B23 A7,A8 A8 A7, =+ + (φ φ φφ )( E1 E1,D7 D7 ), (11) 

 and S S SS SS S S S B2 A2 B21,B12 B12 B13 B21,B22 B22 B23 A7,A8 A8 A7, =+ + (φ φ φφ )( E1 E1,D7 D7 ) . (12) 

Note that the first bracketed term in eqn. 9 and 10 accounts for survival of fish taking either 

Miner Slough (SB12SB13) or Steamboat Slough (SB22SB23) weighted by the joint probability of 

surviving and taking each of these routes (φhi,jk).

We used an approach similar to Newman and Brandes (2001) to quantify survival 

through each migration route relative to survival of fish that migrate within the Sacramento 

River:

A

h

h

S

S

θ =

 

h ≠ A. (13) 

 

We measured each route relative to route A because the Sacramento River is considered the 

primary migration route. For Georgiana Slough, θD is nearly analogous to θ estimated by 

Newman and Brandes (2001), who estimated the ratio of recovery rates of coded wire tagged fish 

released into Georgiana Slough and the Sacramento River near A4. Survival through the Delta 

for route h is equal to Route A when θh = 1, and survival through route h is less (greater) than 

Route A when θh is less (greater) than one. We interpreted survival through route h as

significantly different than Route A at α = 0.05 when θh = 1 fell outside the 95-percent 

confidence interval of ˆθh . 
14

Results

River Conditions and Migration Timing

River conditions differed between the December and February release groups and 

influenced travel times of juvenile salmon through the Delta (fig. 4). For fish released in 

December, tagged fish passed the two river junctions when discharge of the Sacramento River at

Freeport was about 10,000 ft3

/s. In contrast, fish released in February migrated when discharge 

decreased from about 40,000 to 20,000 ft3/s, during the descending limb of a large freshet (fig. 

4). These environmental conditions substantially influenced the travel times of juvenile salmon 

through the Delta.

The first release group took the longest to pass the second river junction (Stations A4, C1, 

and D1 in fig. 2). The median travel time from release to this river junction was 16.8 d with an 

interquartile range (25th to 75th percentile) of 13.2–29.5 d (n = 81, fig. 4). The Delta Cross 

Channel was open at the time of release, but closed between 0955 on December 6 and 1001 on 

December 7. The Delta Cross Channel was then re-opened at 1002 on December 7, 2009, and 

closed again at 0958 hours on December 15, 2009, and remained closed for the balance of the 

study (fig. 4). Given the long travel times to this junction and the median arrival date of 

December 20, 2009, a substantial fraction of this release group passed the second river junction 

after Delta Cross Channel had closed (fig. 4). 

The second release group traveled more quickly to river junction 2 compared to the first 

release group. Median travel times for R2 (7.3 d, n = 79) were less than one-half that of R1 (16.8 

d, n = 81), and the interquartile range was narrower (3.5–11.7 d for R1, 13.2–29.5 d for R2; fig. 

4). In addition, median travel time to Freeport (site A2 in fig. 2), the first detection site in the 

Delta, was 14.8 d for R1 (n = 108), but only 1.6 d for R2 (n = 124), suggesting that the first 

release group delayed initiation of migration. Given that river discharge was similar for both 

release groups, these findings provide evidence that the first release group may not have been 

actively migrating smolts at the time of release.

Both February release groups (R3 and R4) traveled substantially faster to the second river 

junction than the December release groups (R1 and R2), probably due to higher discharge. 

Median travel times were 1.1 and 1.3 d for R3 and R4, with interquartile ranges of 0.98–1.2 d (n = 

55) and 1.2–1.6 d (n = 56) for R3 and R4, respectively. 

Due to higher river discharge in February, the February release groups also traveled more 

quickly to the exit of the Delta (Chipps Island) and had a more compressed travel time 

distribution (fig. 4). The December release groups had median travel times to Chipps Island of 

30.1 d (n = 47) and 19.2 d (n = 49), respectively, for R1 and R2 (fig. 4). In contrast, median travel 

times for the February release groups were 6.2 d (n = 105) and 5.0 d (n = 112), respectively, for 

R3 and R4 (fig. 4). 

Detection Probabilities

For the December release groups, as in past studies (Perry, 2010; Perry and others, 2010), 

detection probabilities at many telemetry stations were high (see appendix A, table A1). 

However, during high flows in February, detection probabilities in the upper Delta were 

considerably lower than previously observed (see appendix, table A1). For example, estimates of 

detection probabilities at Freeport, PA2, were 1.0 for R1 and R2, and 0.823 for R4, but only 0.18 

for R3, the group released during the highest river discharge. As another example, estimates of 
15

 

Figure 4. River discharge, water exports, and Delta Cross Channel discharge during the migration period 

of tagged juvenile Chinook salmon migrating through the Sacramento-San Joaquin River Delta during 

winter of 2009–10. Boxplots show the distribution of arrival dates at Junction 2 on the Sacramento River 

and at Chipps Island, the terminus of the Delta. The symbols R1-R4 are plotted at the release date.

Whiskers represent the 10th and 90th percentiles, the box encompasses the 25th to 75th percentiles, and 

the line bisecting the box is the median arrival date. River discharge (solid line) is tidally filtered, daily 

discharge of the Sacramento River at Freeport (near telemetry station A2), Delta Cross Channel discharge 

(dotted line) is the tidally filtered daily discharge, and water exports (dashed line) are the total daily 

discharge of water exported from the Delta at the pumping projects.
16

PA4 were 0.98, 0.99, 0.33, and 0.16 for R1-R4, respectively. These low detection probabilities 

influenced the precision of reach-specific survival estimates. For example, standard errors 

estimates for SA3 were 0.013, 0.031, 0.104, and 0.098 for R1-R4, respectively, despite larger 

sample sizes for R3 and R4 (appendix A, table A1). High flows likely caused tagged juvenile 

salmon to move very quickly past telemetry stations, causing low detection probabilities. The 

increased flow also may have decreased the effective detection range of receivers due to 

increased acoustic noise.

Route-Specific Survival through the Delta

Model selection criteria allowed us to pool parameters between release sites to improve 

precision of survival estimates. AIC for full model was 5.6 and 4.9 units larger than AIC for the 

reduced model, respectively for R1 and R2, suggesting no differences in survival or detection 

probabilities between Elkhorn Boat Ramp and Georgiana Slough release sites.

Compared to the differences in travel time, we found relatively little difference in 

survival through the Delta among release groups (table 2). Estimates of SDelta ranged from 0.374 

to 0.524 among release groups, a difference of 0.15 (table 2). However, differences in SDelta

among release groups were inconsistent with their travel times. For example, R1 and R3 exhibited 

similar survival through the Delta (table 2), but median travel times for R1 were five times that of 

R3 (fig. 2). Survival per day, expressed as a function of mean travel time from Freeport (station 

A2) to Chipps Island (station A9), was 0.949, 0.937, 0.881, and 0.920 for R1–R4, respectively, 

illustrating that survival rates per unit time were lower for the February release groups.

Patterns in route-specific survival were consistent across releases. Survival was highest 

for fish remaining in the Sacramento River and lowest for fish entering the interior Delta (fig. 5). 

As in previous years, survival for Sutter and Steamboat Sloughs combined was lower than for the 

Sacramento River for the December releases (R1 and R2), but was similar between these routes 

for the February releases (R3 and R4). Closer examination of this pattern revealed that survival of 

fish entering Steamboat Slough closely tracked survival for the Sacramento River; however, fish 

entering Sutter Slough exhibited lower survival than fish entering either Steamboat Slough or the 

Sacramento River (table 2, fig. 6). Furthermore, the difference in survival between Sutter and 

Steamboat Sloughs for the February release groups was less than the December release groups 

(table 2, fig. 6). These findings suggest that the increase in route specific survival for Sutter and 

Steamboat Sloughs for February release groups was driven by an increase in survival in Sutter 

Slough. 

Cumulative survival as a function of distance traveled helps to compare differences in 

survival among migration routes and in different regions of the Delta (fig. 7). When mortality 

rate per unit distance traveled is constant, cumulative survival plotted on a log scale yields a 

straight line. However, slopes become more negative (that is, become steeper) moving from 

Freeport to Chipps Island, indicating that mortality rate per kilometer increases as fish transition 

from the upper to lower Delta (fig. 7). Specifically, the shallowest slopes (lowest mortality rates) 

occurred between Freeport (A2) and the second river junction (A4). Slopes become steeper in the 

tidal zone (A4–A9), indicating higher mortality rates per unit distance. Migration distances also 

vary among routes with Steamboat Slough being the shortest route to Chipps Island (67.4 km) 

and Georgiana Slough being the longest (94.1 km). Thus, if fish using different routes had the 

same mortality rate per unit distance, we would expect total survival to be lower for fish entering 

the interior Delta simply due to a longer migration distance. However, we observed the steepest 

slopes for fish entering the interior Delta, between station D4 and A9, indicating higher mortality 
17

Table 2. Route-specific survival through the Sacramento–San Joaquin River Delta (Sh) and the probability 

of migrating through each route (Ψh) for acoustically tagged fall-run juvenile Chinook salmon released

December 2–5, 2009 (R1) and December 16–19, 2009 (R2). Also shown is population survival through the 

Delta (SDelta), which is the average of route-specific survival weighted by the probability of migrating through 

each route.

Migration route Sh (SE)

95-percent

confidence

interval Ψh (SE)

95-percent

confidence

interval

R1: December 2-5, 2009

A) Sacramento R. 0.584 (0.057) 0.472, 0.696 0.512 (0.048) 0.417, 0.606

B) Sutter & Steamboat S. 0.446 (0.076) 0.297, 0.595 0.223 (0.039) 0.146, 0.300

 B1) Sutter S. 0.336 (0.090) 0.159, 0.512 0.134 (0.032) 0.071, 0.197

 B2) Steamboat S. 0.612 (0.077) 0.461, 0.764 0.089 (0.027) 0.036, 0.142

C) Delta Cross Channel 0.236 (0.080) 0.080, 0.392 0.038 (0.019) 0.001, 0.074

D) Georgiana S. 0.248 (0.047) 0.156, 0.340 0.227 (0.041) 0.147, 0.307

SDelta (All routes) 0.464 (0.044) 0.377, 0.551

R2: December 16-19, 2009

A) Sacramento R. 0.510 (0.059) 0.395, 0.625 0.392 (0.045) 0.303, 0.481

B) Sutter & Steamboat S. 0.345 (0.061) 0.225, 0.465 0.319 (0.043) 0.234, 0.404

 B1) Sutter S. 0.302 (0.065) 0.176, 0.429 0.243 (0.044) 0.158, 0.328

 B2) Steamboat S. 0.483 (0.087) 0.312, 0.653 0.076 (0.028) 0.020, 0.131

C) Delta Cross Channel NA NA 0.000 (0.000) NA

D) Georgiana S. 0.223 (0.040) 0.144, 0.301 0.289 (0.042) 0.207, 0.371

SDelta (All routes) 0.374 (0.040) 0.296, 0.452

R3: January 31, 2010

A) Sacramento R. 0.485 (0.059) 0.371, 0.600 0.449 (0.045) 0.361, 0.537

B) Sutter & Steamboat S. 0.468 (0.062) 0.347, 0.589 0.447 (0.049) 0.352, 0.542

 B1) Sutter S. 0.432 (0.079) 0.276, 0.588 0.242 (0.091) 0.063, 0.420

 B2) Steamboat S. 0.510 (0.084) 0.346, 0.675 0.205 (0.085) 0.038, 0.372

C) Delta Cross Channel NA NA 0.000 (0.000) NA

D) Georgiana S. 0.179 (0.074) 0.034, 0.324 0.104 (0.022) 0.061, 0.148

SDelta (All routes) 0.446 (0.041) 0.365, 0.526

R4: February 5, 2010

A) Sacramento R. 0.577 (0.043) 0.492, 0.662 0.600 (0.038) 0.526, 0.673

B) Sutter & Steamboat S. 0.550 (0.061) 0.430, 0.669 0.221 (0.030) 0.162, 0.279

 B1) Sutter S. 0.508 (0.076) 0.359, 0.657 0.135 (0.027) 0.082, 0.188

 B2) Steamboat S. 0.616 (0.071) 0.476, 0.755 0.086 (0.022) 0.044, 0.128

C) Delta Cross Channel NA NA 0.000 (0.000) NA

D) Georgiana S. 0.314 (0.075) 0.167, 0.461 0.179 (0.030) 0.120, 0.239

SDelta (All routes) 0.524 (0.034) 0.457, 0.591
18

0.0 0.2 0.4 0.6 0.8 1.0

0.512 0.223 0.038 0.227

A

B

C D

R 1

0.392 0.319 0.289

A

B

D

R2

0.0 0.2 0.4 0.6 0.8 1.0

0.449 0.447 0.104

A B

D

R 3

0.600 0.221 0.179

A B

D

R4

h (Probability of migrating through route h)

Sh (Probability of surviving Delta through route h )

Figure 5. Probability of surviving migration through the Sacramento-San Joaquin River Delta (Sh) for each 

of four migration routes for tagged late-fall juvenile Chinook salmon migrating from the Sacramento River. 

The width of each bar shows the fraction of fish migrating through each route (h), and the total area under 

the bars yields SDelta. Labels A–D represent the Sacramento River, Steamboat and Sutter Sloughs, the 

Delta Cross Channel, and Georgiana Slough, respectively. 
19

Figure 6. Comparison of route-specific survival between the Sacramento River (A), Sutter Slough (B1), and 

Steamboat Slough (B2) for late-fall Chinook salmon tagged and released in December 2009 (R1 and R2) 

and February 2010 (R3 and R4).
20

Figure 7. Cumulative survival for each migration route as a function of distance traveled for juvenile late-fall 

Chinook salmon released in December 2009 (R1 and R2) and February 2010 (R3 and R4). Symbols show 

cumulative survival to each telemetry station (A2 = Freeport and A9 = Chipps Island; see fig. 2 for others) 

for fish traversing different migration routes (A = Sacramento River, B1 = Sutter Slough, B2 = Steamboat 

Slough, C = Delta Cross Channel, D = Georgiana Slough). Distance traveled was calculated using the 

shortest pathway within each migration route. Note that the y-axis is plotted on a log scale. Common slopes 

on a log scale indicate equal mortality rates per unit distance traveled.

0 20 40 60 80 100

0.2 0.4 0.6 0.8 1.0

R1

A2 A3 A4

A7

A9

A7

A9

A7

A9

A4

D4

A9

D4

A9

Migration route

A

B1

B2

C

D

0 20 40 60 80 100

0.2 0.4 0.6 0.8 1.0

R2 A2

A3 A4

A7

A9

A7

A9

A7

A9

A4

D4

A9

0 20 40 60 80 100

0.2 0.4 0.6 0.8 1.0

R3

A2 A3

A4

A7

A9

A7

A9

A7

A9

A4

D4

A9

0 20 40 60 80 100

0.2 0.4 0.6 0.8 1.0

R4

A2 A3 A4

A7

A9

A7

A9

A7

A9

A4

D4

A9

Distance traveled (km from Freeport, Station A2)

Cumulative survival
21

per unit distance than other routes (fig. 7). Taken together, the higher rate of mortality per unit 

distance and the longer distance traveled through the interior Delta acts to reduce survival 

considerably compared to other migration routes. 

Differences in survival expressed as the ratio of survival for each major migration route 

relative to the Sacramento River (that is, θh) supported conclusions based on comparison of 

survival between routes (table 3). For fish entering the interior Delta through the Delta Cross 

Channel or Georgiana Slough, θh = 1 fell outside the 95-percent confidence intervals for all 

releases, supporting the hypothesis that fish entering the interior Delta had significantly lower 

survival than fish entering the Sacramento River (table 3). The combined survival of fish 

entering Sutter and Steamboat Sloughs was significantly lower than the Sacramento River only 

for R2. However, when Sutter and Steamboat Sloughs were analyzed independently of each 

other, θB2 for Steamboat Slough was not significantly different from 1.0 for all releases. In 

contrast, θB1 for Sutter Slough was significantly different from 1.0 for the December releases, but 

not for the February releases.

Table 3. Ratio (θh) of survival through route h (Sh) to survival through the Sacramento River (SA) for 

acoustically tagged late fall-run juvenile Chinook salmon released in December 2–5 and December 16–19,

2009.

Migration route θh (SE) 95-percent

confidence interval θh (SE) 95-percentconfidence interval

R1: December 2-5 R2: December 16-19

B) Sutter & Sutter S. 0.765 (0.122) 0.525, 1.004 0.677 (0.119) 0.443, 0.911

 B1) Sutter S. 0.575 (0.150) 0.281, 0.869 0.593 (0.126) 0.346, 0.840

 B2) Steamboat S. 1.049 (0.117) 0.820, 1.278 0.948 (0.168) 0.619, 1.276

C) Delta Cross Channel 0.404 (0.140) 0.130, 0.679 NA NA

D) Georgiana S. 0.425 (0.087) 0.255, 0.595 0.437 (0.087) 0.266, 0.607

R3: January 30 R4: February 5

B) Sutter & Sutter S. 0.964 (0.168) 0.635, 1.292 0.952 (0.114) 0.728, 1.176

 B1) Sutter S. 0.890 (0.195) 0.507, 1.272 0.880 (0.139) 0.608, 1.152

 B2) Steamboat S. 1.051 (0.202) 0.656, 1.447 1.066 (0.129) 0.813, 1.319

C) Delta Cross Channel NA NA NA NA

D) Georgiana S. 0.369 (0.151) 0.073, 0.664 0.545 (0.139) 0.272, 0.817

Migration Routing

Migration routing varied considerably among release groups. The Delta Cross Channel 

was closed for all release groups except R1, and only 3.8 percent of this release group entered the 

Delta Cross Channel. However, due to long travel times, only 18.5 percent of this release group 

passed the Delta Cross Channel while the gates were open (table 4). Of the fish that passed the 

Delta Cross Channel while the gates were open, 20 percent entered the Delta Cross Channel, 

which is consistent with previous studies (table 4).
22

Table 4. Probability of migrating through each route (Ψh) for acoustically tagged late fall-run juvenile 

Chinook salmon released in December 2009 as a function of gate position when fish passed the Delta 

Cross Channel. 

[Only 18.5 percent of fish passed the cross channel when it was open (ωopen = 0.185, SE = 0.043)] 

Cross channel open Cross channel closed

Migration route Ψh (SE)

95-percent

confidence

interval Ψh (SE)

95-percent

confidence

interval

A) Sacramento R. 0.521 (0.097) 0.330, 0.713 0.510 (0.052) 0.408, 0.612

B) Sutter & Steamboat S. 0.223 (0.039) 0.146, 0.300 0.223 (0.039) 0.146, 0.300

C) Delta Cross Channel 0.204 (0.088) 0.031, 0.378 NA

D) Georgiana S. 0.051 (0.049) -0.046, 0.148 0.267 (0.047) 0.195, 0.348

The fraction of fish entering the interior Delta for the December releases, during low 

flows, was higher than for the February releases. Routing probabilities for Sutter and Steamboat 

Sloughs affect the proportion of fish entering the interior Delta because fish entering Sutter and 

Steamboat Sloughs bypass the entrance to the interior Delta. For example, R3 exhibited the 

highest fraction of fish entering Sutter and Steamboat Sloughs (45 percent) and consequently the 

lowest fraction entering the interior Delta (10.4 percent) because only about one-half of this 

release group remained in the Sacramento River. Route entrainment probabilities at the second 

river junction also influence the fraction of the population entering the interior Delta. For 

example, of the fish that arrive at Georgiana Slough with the Delta Cross Channel closed, 34.4, 

42.5, 18.8, and 23.0 percent, entered the interior Delta, respectively, for R1-R4 (see ΨD2,closed in 

the appendix A, table A1). These findings show that entrainment into the interior Delta is higher 

during low flow, a finding consistent with Perry (2010). 

Entrainment into Sutter and Steamboat Sloughs varied considerably among releases 

ranging from 22.1 percent for R2 to 44.7 percent for R3. The majority of fish taking this route 

entered Sutter Slough. Migration route probabilities for Sutter Slough ranged from 13.4 to 24.3 

percent among releases. In contrast, entrainment into Steamboat Slough was 7.6–8.9 percent, 

except for R3 when 20.5 percent entered Steamboat Slough. 

Relative Contributions to SDelta

The fraction of fish using each migration route combined with route-specific survival 

influenced overall survival through the Delta. For example, R2 exhibited the lowest SDelta among 

release groups (0.374) and lowest fraction of fish remaining in the Sacramento River. Because 

the Sacramento River had the highest survival for R1 and R2, reducing the fraction remaining in 

the Sacramento River acts to reduce overall survival through the Delta. For R3 and R4, fish 

entering the interior Delta had considerably lower survival than either the Sacramento River or 

Sutter and Steamboat Sloughs. However, less than 20 percent of fish entered the interior Delta 

resulting in a low contribution of this route to SDelta. 
23

Discussion

This report presents the fourth year of route-specific survival of late-fall Chinook salmon; 

some findings were similar to previous years, but others were contrary to previous findings. 

Similar findings to previous years include: (1) highest Chinook salmon survival in the 

Sacramento River, and lowest survival for routes leading to the interior Delta, (2) Chinook 

salmon survival in Sutter and Steamboat Sloughs lower than that of the Sacramento River during 

December releases, but similar during later releases, and (3) similar patterns of Chinook salmon 

migration routing among years. Findings that differed from previous years include: (1) delayed 

migration for fish released in early December, (2) less-than-expected differences in Chinook 

salmon survival between release groups relative to the differences in river flows experienced by 

each release group, and (3) low detection probabilities for some telemetry stations during the 

high flows of the February 2010 release groups. 

During the 2010 migration year, Chinook salmon survival in the Sacramento River was 

higher than for the migration routes leading to the interior Delta. This finding is particularly 

important given that 2010 was the first year in which some release groups migrated wholly 

during relatively higher river flows. In the previous 3 years, most fish migrated during the lower 

range of Sacramento River flows. Flows during previous years averaged about 10,000 ft3/s at 

Freeport, whereas the February 2010 release group experienced flows ranging from 20,000 to 

40,000 ft3/s at Freeport. Even under the higher flows experienced by this release group, we 

observed lower survival for the interior Delta than the Sacramento River. In addition, ratios of 

survival between these routes were similar among release groups ranging from 0.369 to 0.545 

(table 3). These findings suggest that differences in survival between these migration routes exist 

over a range of flows. 

Although patterns in survival differences among routes remained consistent across years, 

we might have expected a larger difference in survival probabilities relative to the flows and 

travel time differences among release groups. Perry (2010) found that route-specific survival for 

the Sacramento River and Sutter and Steamboat Sloughs was positively correlated to both fish 

size and flow of the Sacramento River. The February release groups were comprised of larger 

fish, migrated during higher flows, and had shorter travel times than the December release 

groups. Given the findings of Perry (2010), we would expect to observe a larger difference in 

survival between release groups, but this was not the case. Differences in travel times suggest 

that the February release group experienced lower survival rates when expressed as survival per 

unit time. A number of factors may have been at play in determining observed survival. One 

potential mechanism is the underlying differences in the study population of fish used during the 

December releases relative to the February releases. Our previous analyses, and the December 

release group of this study, were comprised of fish tagged at Coleman National Fish Hatchery.

This population closely matches the rearing and holding conditions experienced by the untagged 

hatchery population. In contrast, fish used for the February release group were transported to 

U.C. Davis and reared under different conditions than the general population of fish at Coleman 

National Fish Hatchery. The February release group was held at U.C. Davis for up to 2 weeks 

following tagging before being transported to the release site. Release protocols also differed 

between release groups. The December release group was released at 4-hour intervals over a 24-

hour period in order to distribute fish over the tidal and diel cycle, whereas the February release 

group was entirely released at night in a single batch. Thus, in addition to being substantially 

larger, differences in rearing history and release pattern may have introduced variation in
24

survival among release groups. Last seasonal differences other than flow (for example, predator 

densities) may account for differences in survival among release groups. 

Examining cumulative survival provided insights into the manner in which migration 

distance and mortality per unit distance interact to affect total survival for each migration route.

For fish migrating through the interior Delta, which is the longest migration route, we found that 

mortality rate per unit distance was higher than other routes. One way of interpreting this finding 

is that survival through the interior Delta would be lower than other routes, even if migration 

distance was the same among routes. Alternatively, if mortality rates per unit distance had been 

the same among routes, survival through the interior Delta would be lower due to a longer 

migration distance. Higher mortality per unit distance combined with longer migration distance 

provides one mechanism for explaining the consistently lower survival for fish entering the 

interior Delta relative to the Sacramento River.

The pattern of cumulative survival with respect to distance also is consistent with the 

predator encounter rate model proposed by Anderson and others (2005). Under this model, when 

prey migrate through a “gauntlet” of predators, predator-prey encounter rates will be such that 

each prey encounters a predator one time at most. Under these circumstances, predator-prey 

theory predicts that survival will be driven by distance traveled, but not by travel time. In 

contrast, when prey migration speeds are slow relative to predator swimming speeds such that 

multiple encounters are possible, then the situation reverses: the probability of survival becomes 

dependent on travel time. This hypothesis is consistent with the steepening slope between 

cumulative survival and distance traveled as fish transition from the upper to lower Delta (fig. 7).

Within our study area, the Sacramento River transitions from river-driven discharge in the 

uppermost reaches to tidally driven discharge in the lower reaches. Coincident with this 

transition, fish movement patterns shift from downstream-only movements to both upstream and 

downstream movements in the lower reaches of the Delta. Thus, in lower reaches of the Delta, 

fish may pass through a given reach more than once. This process could increase predator 

encounter rates relative to the length of each reach, therefore increasing mortality rates per unit 

distance.

The high flows during the third and fourth releases probably caused low detection 

probabilities relative to the first two releases. Low detection probabilities occurred because of a 

combination of the tag design and the proofing algorithm. At high flows, it is possible for a fish 

to be moving at such speeds that the tag “pulses” zero or one time while in the detection zone of 

a hydrophone. For example, we observed numerous fish with only a single detection at a 

hydrophone, which fails our criterion for a valid detection event (a minimum of two detections).

Although many of these detections may have been valid, relaxing this criterion increases the risk

of accepting false positive detections. Because including false positive detection introduces bias 

into survival estimates, we elected to maintain our criterion at a minimum of two detections. 

Low detection probabilities suggest that the pulse rates of these transmitters may have been too 

slow for the high river flows and water velocities observed in February 2010. Future studies 

should consider reducing the pulse rate to increase detection probabilities during high flows. 

Instream acoustic noise also may have contributed to the low detections probabilities. Increased 

flows often decrease detection range of VR2 receivers. The release strategy also may have 

affected tag detection for the February group. Given the number of tagged fish released in a 

single batch, it is possible that tag collisions occurred at telemetry stations first encountered by 

fish. For tags to be detected, fish would have to be within receiver range a greater period of time 

to account for the tag signals potentially canceling each other out. 
25

We observed that entrainment probabilities for routes leading to the interior Delta (ΨC2

and ΨD2, table A1 in appendix A) were lower during the high flows experienced by the February 

release groups, which is consistent with an inverse relationship between flow and entrainment 

probability at this river junction. Perry (2010) found that daily entrainment probabilities 

decreased as the proportion of river flow entering the interior Delta increased. In turn, the 

fraction of discharge entering the interior Delta increases as flow decreases. Because a lower 

fraction of the population entered the interior Delta during February releases, this route 

contributed less to SDelta relative to December release groups, thereby increasing overall survival 

through the Delta. For example, had migration route probabilities for the interior Delta for R3

(ΨD = 0.104) been similar to R2 (ΨD = 0.289), SDelta would have been 0.390 instead of 0.445. 

This example illustrates the interplay between migration routing and overall survival in the 

Delta.

Determining which factors influence the migration and survival dynamics of juvenile 

Chinook salmon is critical to the management and recovery of salmon in the Central Valley. 

After 4 years of study, patterns in survival and movement dynamics are beginning to emerge.

Such information helps to inform management actions that will improve survival of juvenile 

salmonid populations migrating through the Sacramento-San Joaquin River Delta.

Acknowledgments

Tagging of juvenile salmon, ultrasonic station deployment and interrogation, and tagdetection database maintenance were supported by a grant from the California Bay-Delta 

Authority by Agreement No. U-05-SC-047 (A. Peter Klimley and Bruce MacFarlane, PIs). We 

thank Kevin Niemela, Kurtis Brown, and Scott Hamelburg of U.S. Fish and Wildlife Service and 

the staff of Coleman National Fish Hatchery for providing the late-fall Chinook and logistical 

support at the hatchery for this study. We are grateful to the following staff of the U.S. Fish and 

Wildlife Service in Stockton, California, for assisting with transport, holding, and release of 

tagged fish: Phil Voong, Dustin Dinh, Denise Barnard, Amber Aguilera, Pete Hrodey, Mike 

Marshall, Amy Combs and Patricia Brandes. Lynne Casal, USGS, was instrumental in assisting 

with report construction and formatting. 

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28

Appendix A 

Table A1. Parameter estimates (SE) under the reduced model for releases of acoustically tagged late-fall 

juvenile Chinook salmon in December, 2009 (R1 and R2) and February, 2010 (R3 and R4). 

[Parameters not estimated are indicated by an “NA” in the estimate column, and parameters fixed at a constant value 

are noted by an “NA” in parentheses] 

Parameter R1 R2 R3 R4

SA1 0.683 (0.036) 0.806 (0.032) 1.050 (0.061) 0.951 (0.018)

SA2 0.981 (0.013) 0.878 (0.031) 1.052 (0.100) 0.944 (0.039)

SA3 0.944 (0.025) 0.990 (0.013) 0.813 (0.104) 1.011 (0.098)

SA4, open 0.932 (0.099) NA NA NA

SA4, closed 0.915 (0.053) 0.816 (0.067) 0.838 (0.069) 0.790 (0.097)

SA7 0.893 (0.053) 0.910 (0.059) 0.856 (0.034) 0.899 (0.034)

SA8 0.784 (0.061) 0.817 (0.064) 0.860 (0.035) 0.876 (0.034)

SB11 0.733 (0.114) 0.696 (0.091) 0.748 (0.128) 0.876 (0.089)

SB12 0.900 (0.095) 0.800 (0.126) 0.933 (0.064) 0.900 (0.067)

SB13 0.690 (0.163) 0.654 (0.180) 0.797 (0.101) 0.881 (0.083)

SB21 1.000 (NA) 0.899 (0.107) 0.840 (0.122) 1.000 (NA)

SB22 1.000 (NA) 0.852 (0.097) 0.903 (0.057) 0.867 (0.073)

SB23 0.941 (0.091) 1.000 (NA) 0.944 (0.035) 0.982 (0.054)

SC1 0.750 (0.217) NA NA NA

SD1,Sac,open 1.000 (NA) NA NA NA

SD1,Sac,closed 0.870 (0.070) 0.889 (0.057) 0.962 (0.197) 0.804 (0.082)

SD1,Geo 0.667 (0.058) 0.757 (0.052) NA NA

SD2,Sac 0.883 (0.052) 0.837 (0.051) 0.714 (0.171) 1.017 (0.102)

SD2,Geo 0.883 (0.052) 0.837 (0.051) NA NA

SD4,Sac 0.360 (0.062) 0.511 (0.065) 0.313 (0.116) 0.448 (0.100)

SD4,Geo 0.360 (0.062) 0.511 (0.065) NA NA

SD7,Sac 1.000 (NA) 0.800 (0.079) 1.000 (NA) 0.908 (0.107)

SD7,Geo 1.000 (NA) 0.800 (0.079) NA NA

SE1,D7,Sac 0.640 (0.202) 0.799 (0.210) 0.482 (0.109) 0.701 (0.173)

SE1,D7,Geo 0.640 (0.202) 0.799 (0.210) NA NA

SE1,A8,Sac 1.000 (NA) 0.523 (0.153) 1.000 (NA) 1.000 (NA)

SE1,A8,Geo 1.000 (NA) 0.523 (0.153) NA NA

ωopen 0.185 (0.043) 0.000 (NA) 0.000 (NA) 0.000 (NA)

ΨA1 0.777 (0.039) 0.681 (0.043) 0.553 (0.049) 0.779 (0.030)

ΨB11 0.134 (0.032) 0.243 (0.044) 0.242 (0.091) 0.135 (0.027)

ΨB21 0.089 (0.027) 0.076 (0.028) 0.205 (0.085) 0.086 (0.022)

ΨA2,open 0.671 (0.121) NA NA NA

ΨA2,closed 0.656 (0.058) 0.575 (0.055) 0.812 (0.037) 0.770 (0.038)

ΨC2,open 0.263 (0.113) NA NA NA

ΨD2,open 0.066 (0.064) NA NA NA

ΨD2,closed 0.344 (0.058) 0.425 (0.055) 0.188 (0.037) 0.230 (0.038)

φB21,B12 0.100 (0.095) 0.000 (NA) 0.000 (NA) 0.000 (NA)

φB21,B22 0.900 (0.095) 0.899 (0.107) 0.840 (0.122) 1.000 (NA)

φB11,B12 0.600 (0.126) 0.346 (0.093) 0.290 (0.123) 0.741 (0.116)

φB11,B22 0.133 (0.088) 0.350 (0.095) 0.458 (0.143) 0.135 (0.089)

φA7,A8 0.796 (0.060) 0.769 (0.067) 0.700 (0.038) 0.811 (0.039)

φA7,E1 0.096 (0.038) 0.141 (0.054) 0.156 (0.033) 0.088 (0.029)

φD4,D7,Sac 0.266 (0.056) 0.339 (0.059) 0.250 (0.109) 0.325 (0.093)
29

φD4,D7,Geo 0.266 (0.056) 0.339 (0.059) NA NA

φD4,E1,Sac 0.094 (0.037) 0.172 (0.048) 0.063 (0.061) 0.124 (0.059)

φD4,E1,Geo 0.094 (0.037) 0.172 (0.048) NA NA

PA2 0.946 (0.021) 0.915 (0.026) 0.180 (0.026) 0.823 (0.027)

PA3 1.000 (NA) 1.000 (NA) 0.171 (0.036) 0.340 (0.039)

PA4 0.979 (0.021) 0.985 (0.015) 0.329 (0.053) 0.156 (0.036)

PA7 0.754 (0.057) 0.651 (0.066) 0.855 (0.030) 0.702 (0.041)

PA8,Sac 0.845 (0.054) 0.858 (0.057) 0.953 (0.022) 0.927 (0.029)

PA8,Geo 1.000 (NA) 0.858 (0.057) NA NA

PA9,Sac 0.860 (0.049) 0.894 (0.041) 0.901 (0.030) 0.906 (0.030)

PA9,Geo 1.000 (NA) 0.894 (0.041) NA NA

PB11 1.000 (NA) 0.900 (0.095) 0.211 (0.094) 0.500 (0.107)

PB12 1.000 (NA) 1.000 (NA) 0.778 (0.098) 0.900 (0.067)

PB21 1.000 (NA) 1.000 (0.186) 0.248 (0.113) 0.627 (0.133)

PB22 1.000 (NA) 0.933 (0.064) 0.372 (0.059) 0.906 (0.063)

PB13 1.000 (NA) 1.000 (NA) 1.000 (NA) 1.000 (NA)

PB23 0.727 (0.134) 0.258 (0.112) 0.910 (0.049) 0.945 (0.053)

PC1 1.000 (NA) 1.000 (NA) 1.000 (NA) 1.000 (NA)

PD1 1.000 (NA) 0.985 (0.015) 0.944 (0.054) 0.867 (0.062)

PD2,Sac 1.000 (NA) 0.956 (0.025) 0.312 (0.116) 0.431 (0.090)

PD2,Geo 0.895 (0.050) 0.956 (0.025) NA NA

PD4,Geo 0.837 (0.073) 0.917 (0.046) NA NA

PD4,Sac 1.000 (NA) 0.917 (0.046) 1.000 (NA) 0.848 (0.098)

PD7,Geo 0.853 (0.078) 1.000 (NA) NA NA

PD7,Sac 0.853 (0.078) 0.816 (0.104) 0.793 (0.106) 0.460 (0.126)

PE1,Sac 0.866 (0.124) 0.521 (0.160) 0.823 (0.112) 0.697 (0.118)

PE1,Geo 1.000 (NA) 1.000 (NA) NA NA

λSac 0.902 (0.038) 0.834 (0.048) 0.849 (0.035) 0.777 (0.039)

λGeo 0.902 (0.038) 0.834 (0.048) NA NA
30

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Perry and others—Survival and Migration Route Probabilities of Juvenile Chinook Salmon, Sacramento-San Joaquin River Delta, Winter of 2009–10—Open-File Report 2012–1200