U.S. Department of the Interior

U.S. Geological Survey

Open-File Report 2018–1118

Prepared in cooperation with the California Department of Water Resources

Survival, Travel Time, and Utilization of Yolo Bypass, 

California, by Outmigrating Acoustic-Tagged Late-Fall 

Chinook Salmon
Cover: Photograph looking southwest over Yolo Bypass (upper right) diverting flood 

water around Sacramento, California, parallel with the Sacramento River. Photograph 

by Chris Austin, Maven's Notebook.
Survival, Travel Time, and Utilization of Yolo Bypass, 

California, by Outmigrating Acoustic-Tagged Late-Fall 

Chinook Salmon 

By Adam C. Pope, Russell W. Perry, Dalton J. Hance, and Hal C. Hansel 

Prepared in cooperation with the California Department of Water Resources

Open-File Report 2018–1118

U.S. Department of the Interior

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

RYAN K. ZINKE, Secretary

U.S. Geological Survey

James F. Reilly II, Director

U.S. Geological Survey, Reston, Virginia: 2018

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Suggested citation:

Pope, A.C., Perry, R.W., Hance, D.J., and Hansel, H.C., 2018, Survival, travel time, and utilization of 

Yolo Bypass, California, by outmigrating acoustic-tagged late-fall Chinook salmon: U.S. Geological 

Survey Open-File Report 2018-1118, 33 p., https://doi.org/10.3133/ofr20181118. 

ISSN 2331-1258 (online)
iii

Contents

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

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

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

Study Area ................................................................................................................................................. 4

Fish Tagging and Transport ....................................................................................................................... 4

Fish Release Strategy................................................................................................................................ 6

Data Processing......................................................................................................................................... 7

Screening and Removal of False Positive Detections............................................................................ 7

Screening and Removal of Detections of Predated Tags ...................................................................... 7

Survival, Routing, and Travel-Time Analysis.............................................................................................. 8

Multistate Mark-Recapture Survival Model ............................................................................................ 8

Travel Time Likelihood......................................................................................................................... 11

Derived Parameters............................................................................................................................. 12

Bayesian Estimation via Hamiltonian Monte Carlo............................................................................... 13

Spatial Distribution and Survival Within the Yolo Bypass ......................................................................... 13

California WaterFix North Delta Diversion Intake Study ........................................................................... 14

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

Survival, Routing, and Travel Time .......................................................................................................... 14

Survival Estimates ............................................................................................................................... 14

Migration Routing Estimates ................................................................................................................ 17

Travel Time Parameter Estimates ....................................................................................................... 19

Mean Daily Survival Probabilities......................................................................................................... 21

Spatial Distribution and Survival within the Yolo Bypass.......................................................................... 22

California WaterFix North Delta Diversion Intake Study ........................................................................... 24

Discussion ................................................................................................................................................... 25

Acknowledgments ....................................................................................................................................... 26

References Cited......................................................................................................................................... 26

Appendix 1. Fundamental Reach-Specific Parameter Estimates................................................................ 29

Figures

Figure 1. Map showing study area, Sacramento-San Joaquin River Delta, California ................................. 5

Figure 2. Instantaneous river flows in Yolo Bypass, in the Sacramento River at Freeport, and in Cache 

Slough taken at 15-minute intervals, with times of release for each of five release groups ........................... 7

Figure 3. Schematic of the multistate mark-recapture model with parameters indexed by state (migration 

route) and sampling occasion........................................................................................................................ 9

Figure 4. Median probability of survival with upper and lower credible limits (the 5th and 95th percentiles of 

the posterior distributions for each parameter, respectively) from Fremont Weir to Chipps Island by route 

through the North Delta, California. ............................................................................................................. 16

Figure 5. Median probability of entrainment with upper and lower credible limits from Fremont Weir to 

Chipps Island, California, by route............................................................................................................... 18

Figure 6. Route-specific travel time quantiles from Fremont Weir to Chipps Island, Sacramento-San 

Joaquin River Delta, California .................................................................................................................... 20

Figure 7. Cross-stream distribution of tagged fish distribution within Yolo Bypass at the I-80 bridge, 

separated by release site, California............................................................................................................ 23
iv

Tables

Table 1. Dates and numbers of acoustically tagged juvenile Chinook salmon released, Sacramento-San 

Joaquin River Delta, California. ..................................................................................................................... 6

Table 2. Derived parameters for route-specific overall survival from the Fremont Weir to Chipps Island, 

Sacramento-San Joaquin River Delta, California......................................................................................... 15

Table 3. Derived parameters for route-specific entrainment probabilities from the Fremont Weir to Chipps 

Island, Sacramento-San Joaquin River Delta, California. ............................................................................ 17

Table 4. Derived parameters for route-specific travel times from the Fremont Weir to Chipps Island, 

Sacramento-San Joaquin River Delta, California......................................................................................... 19

Table 5. Derived parameters for route-specific daily survival from the Fremont Weir to Chipps Island, 

Sacramento-San Joaquin River Delta, California......................................................................................... 21

Table 6. Number of juvenile Chinook salmon used to estimate survival for three Sacramento River reaches 

encompassing proposed North Delta Diversion intakes in the North Delta, Sacramento-San Joaquin River 

Delta, California. .......................................................................................................................................... 24

Table 7. Median reach-specific and cumulative survival estimates, and 95-percent credible intervals by fish 

release and reach for the three proposed water-intake sites, Sacramento-San Joaquin River Delta, 

California. .................................................................................................................................................... 24
v 

Conversion Factors

International System of Units to U.S. customary units 

Multiply By To obtain

Length

millimeter (mm) 0.03937 inch (in.)

meter (m) 3.281 foot (ft) 

kilometer (km) 0.6214 mile (mi)

kilometer (km) 0.5400 mile, nautical (nmi) 

meter (m) 1.094 yard (yd) 

Flow rate

cubic meter per second (m3/s) 70.07 acre-foot per day (acre-ft/d) 

meter per second (m/s) 3.281 foot per second (ft/s) 

meter per day (m/d) 3.281 foot per day (ft/d)

cubic meter per second (m3/s) 35.31 cubic foot per second (ft3/s)

cubic meter per second (m3/s) 22.83 million gallons per day (Mgal/d) 

kilometer per hour (km/h) 0.6214 mile per hour (mi/h)

Mass

gram (g) 0.03527 ounce, avoirdupois (oz)

kilogram (kg) 2.205 pound avoirdupois (lb)

Datums

Vertical coordinate information is referenced to the North American Vertical Datum of 1988 (NAVD 88).

Horizontal coordinate information is referenced to the North American Datum of 1983 (NAD 83).

Supplemental Information

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

Note to USGS users: Use of hectare (ha) as an alternative name for square hectometer (hm2) is restricted to the measurement of 

small land or water areas. Use of liter (L) as a special name for cubic decimeter (dm3) is restricted to the measurement of liquids 

and gases. No prefix other than milli should be used with liter.

Abbreviations

CADWR California Department of Water Resources

CVP

NDD

NMFS

Central Valley Project

North Delta Diversion

National Marine Fisheries Service

SWP

USBR

California State Water Project

U.S. Bureau of Reclamation

USGS U.S. Geological Survey
vi 
1 

Survival, Travel Time, and Utilization of Yolo Bypass, 

California, by Outmigrating Acoustic-Tagged Late-Fall 

Chinook Salmon 

By Adam C. Pope, Russell W. Perry, Dalton J. Hance, and Hal C. Hansel 

Abstract

Juvenile Chinook salmon (Oncorhynchus tshawytscha) migrating through California's

Sacramento-San Joaquin River Delta toward the Pacific Ocean face numerous challenges to their 

survival. The Yolo Bypass is a broad floodplain of the Sacramento River that floods in about 70 

percent of years in response to large, uncontrolled runoff events. As one of the routes juvenile salmon 

may utilize, the Yolo Bypass has recently received attention for having potential benefit to rearing and 

migrating salmon. Consideration is being given to a plan to build a cut or “notch” in the Fremont Weir 

to increase juvenile salmon access to the Yolo Bypass. To help provide information about the potential 

benefit of such a plan, we analyzed data from a telemetry study conducted in February and March 

2016 by the U.S. Geological Survey and California Department of Water Resources to estimate 

entrainment into and distribution of juvenile Chinook salmon within the Yolo Bypass, and to compare 

survival and travel time through the Yolo Bypass to other routes in the Delta. We also estimated 

juvenile Chinook salmon survival through three short reaches of the Sacramento River where the 

proposed California WaterFix North Delta Diversion intakes would divert water to export facilities to 

provide baseline information against which any effects of those intakes could be measured in the 

future. 

We found that entrainment into the Yolo Bypass varied widely and was quite high only at the 

peak of the March 2016 flood. Spatial distribution of juvenile Chinook salmon within the Yolo Bypass 

was fairly even for fish entering the Yolo Bypass over the Fremont Weir, but increasingly skewed 

toward the east bank for fish released within the Yolo Bypass. Survival within Yolo Bypass was not 

significantly different for fish based on spatial distribution. Survival through the Delta for fish 

migrating through the Yolo Bypass was generally on par with the weighted survival through the Delta 

of fish migrating through all other routes. Survival was highest for fish remaining in the Sacramento 

River and lowest for those entrained into the Interior Delta via Georgiana Slough. Survival through the 

short section of the Sacramento River near the proposed North Delta Diversion intakes was high.
2 

Introduction

Juvenile Chinook salmon (Oncorhynchus tshawytscha) migrating from their natal tributaries 

toward the Pacific Ocean are subject to numerous factors affecting their migration timing, migration 

route, and survival. Several factors are influenced by the regulation of rivers through which these fish 

migrate. For example, flow regulation can impact river temperature and turbidity, which can in turn 

affect availability of thermal refugia or exposure to predation (Raymond, 1988; Smith and others, 

2003). Diversion of flows can influence the migration route used by juvenile salmon, which can 

ultimately influence overall population survival if there is a substantial difference in survival among 

routes (Skalski and others, 2002; Perry and others, 2015). Understanding the mechanisms by which 

migration timing, route selection, and survival are affected, either directly or indirectly, by the 

regulation of river systems can help managers make decisions that are more likely to benefit these 

populations. 

The Sacramento-San Joaquin River Delta (hereafter, “Delta”) in the Central Valley of 

California is a network of both natural and man-made channels connecting the Sacramento and San 

Joaquin Rivers with the San Francisco Bay on their way toward the Pacific Ocean (fig. 1). Juvenile 

salmon migrating downstream through the Sacramento River must navigate the Delta on their seaward 

journey. The Delta also supports both the Central Valley Project (CVP) and California State Water 

Project (SWP), which supply agricultural and drinking water to much of California by diverting river 

water to aqueducts via pumping stations in the southern Delta. 

Several factors affect juvenile salmon survival during migration, either directly or indirectly.

Since navigation through the Delta affords multiple routes, the route travelled is important in 

determining the probability a fish survives to reach the ocean. For example, predator density in the 

Delta is thought to vary among migration routes (Turner and Chadwick, 1972; Nobriga and others, 

2005), driving variation in route-specific survival. Likewise, survival can be affected indirectly 

through the amount of time it takes for a fish to navigate through the Delta. For instance, a fish that 

remains in the mainstem Sacramento River is likely to reach San Francisco Bay sooner than one that 

enters Georgiana Slough, which diverts fish to the “Interior Delta” (the region to the south of the 

mainstem Sacramento River; fig. 1) where tidal influences, multiple side channels, and water-pumping 

stations can each act to disorient and slow migrating fish (Brandes and McLain, 2001; Newman and 

Brandes, 2010; Perry and others, in press).
3 

One potential route for downstream migrating juvenile salmon is the Yolo Bypass, a broad 

floodplain (64-km-long and 4.8-km-wide) of the Sacramento River that floods in about 70 percent of 

years in response to large, uncontrolled runoff events (Sommer and others, 2008). Studies have 

suggested that access to the Yolo Bypass floodplain habitat can increase fitness and survival of 

migrating juvenile salmon (Sommer and others, 2001a, 2001b, 2005). In addition to accessing highquality rearing habitat, juvenile salmon entrained into the Yolo Bypass avoid migration through the 

Interior Delta, where survival has been shown to be significantly lower than for other routes (Perry and 

others, 2010, 2013). As a result, consideration is being given to providing an intake or “notch” in the 

Fremont Weir as a management action to benefit salmon populations in the Sacramento River under 

Yolo Bypass Salmonid Habitat Restoration and Fish Passage Implementation Plan (U.S. Bureau of 

Reclamation and California Department of Water Resources, 2012). Fremont Weir is a 2.9-km-long 

concrete structure that, when overtopped by the Sacramento River, leads to flooding of the Yolo 

Bypass, providing access to juvenile salmon. However, there is little direct information available on 

how migrating salmon utilize the Yolo Bypass, including the proportion of fish entering Yolo Bypass, 

survival within the bypass, and the spatial distribution of fish migrating through the Yolo Bypass. 

In addition to serving as the migratory pathway for juvenile anadromous fishes, the Delta is 

also the hub of California’s water delivery system. California WaterFix is a proposed multi-billiondollar Sacramento River water project designed to update the SWP and coordinated operations of the 

CVP. The WaterFix Project proposal includes the construction of three water diversion intakes named 

the North Delta Diversion intakes, among other proposed new infrastructure. The new intakes would 

be located on the east bank of the Sacramento River at river kilometers (rkms) 66.1, 63.4, and 59.2 

(fig. 1). Together, the intakes would be capable of diverting a maximum combined total flow of 254.9 

m3/s (9,000 ft3/s). The intakes would include state-of-the-art fish screens to minimize fish entrainment 

and enable the SWP and CVP to coordinate South and North Delta facilities operations in a way that 

would enhance protective measures for native fish. The water diverted by the intakes would be carried 

30 miles by two 40-foot-diameter underground pipelines to the Clifton Court Forebay where two 

proposed pumping plants would be built to maintain optimum water levels in the forebay for the 

existing SWP and CVP pumping facilities (ICF International, 2016). Baseline information on survival 

of juvenile salmon through the proposed intake reaches will provide important context to future 

management. 

To provide information on the potential benefit of management actions that increase salmonid 

access to Yolo Bypass, the U.S. Geological Survey (USGS), in cooperation with CADWR, undertook 

a telemetry study using acoustically tagged juvenile Chinook salmon to estimate the probability of 

entrainment through a project notch and survival within the Yolo Bypass before, during, and after a 

flood event during the migration season of 2016. To maximize the utility of this study, we used data 

arising from the study for three distinct objectives: (1) to estimate and compare route-specific survival 

and travel time of juvenile Chinook salmon utilizing the Yolo Bypass to that of fish using other 

available routes in the North Delta during the same period of time; (2) to determine the spatial 

distribution and difference in survival of fish along an east-west gradient within the Yolo Bypass; and, 

(3) to evaluate fine-scale reach-to-reach survival of Chinook salmon remaining in the mainstem 

Sacramento River in the vicinity of the proposed California WaterFix North Delta Diversion intakes. 
4 

Methods

Study Area

We evaluated the potential benefit of the Yolo Bypass to migrating juvenile salmon in the 

context of the branching network of channels of the North Sacramento-San Joaquin Delta. Multiple 

migration routes are available to juvenile salmon migrating oceanward through the North Delta. In 

addition to remaining in the mainstem Sacramento River, fish may utilize one or more alternative 

migration routes. The Yolo Bypass begins at the Sacramento River just upstream from Verona at the 

Fremont Weir. When the weir is overtopped, fish can be entrained into the Yolo Bypass, which rejoins 

the Sacramento River near Rio Vista via Cache Slough. Sutter and Steamboat Sloughs diverge from 

the mainstem Sacramento River downstream from Freeport, subsequently connect via Miner Slough 

and, like the Yolo Bypass, rejoin the Sacramento River near Rio Vista. For fish that remain in the 

Sacramento River, subsequent divergences are the Georgiana Slough and, when its radial gate is open, 

the Delta Cross Channel near Walnut Grove. These two channels join the Mokelumne River, the lower 

San Joaquin River, and the channels of the Interior Delta, which in turn lead to either of the CVP or 

SWP export facilities or rejoin the Sacramento River near Chipps Island (fig. 1). 

A network of acoustic telemetry stations were deployed throughout the North Delta to monitor 

acoustically tagged juvenile salmon as they migrated to the ocean. Each telemetry station consisted of 

one or more acoustic tag detecting hydrophones (Vemco, Ltd.; Models VR2W, HR2). The number of 

hydrophones deployed at each station varied depending on the number needed to maximize detection 

probability. Except for Yolo Bypass, hydrophones were located just downstream of each major 

channel junction in each route. No hydrophones were deployed in the Yolo Bypass immediately below 

its entrance via Fremont Weir due to logistical challenges associated with monitoring the entire length 

of Fremont Weir. Instead, an array of hydrophones was deployed along the Interstate 80 bridge 

(hereinafter, “I-80”) across the section flooded by the Yolo Bypass (fig. 1). Additional hydrophones 

were located at exits of migration routes, including where Sutter Slough, Steamboat Slough, and the 

Yolo Bypass rejoin the Sacramento River, as well as at the exit of Georgiana Slough into the 

Mokelumne River (fig. 1). Multiple hydrophones were deployed in the Sacramento River near Chipps 

Island to form a pair of detection arrays at the study area’s furthest downstream point. Finally, multiple 

hydrophones were in the Sacramento River between Freeport and the junction with Sutter Slough. 

These stations were positioned to bracket each of three proposed sites for the California Waterfix 

North Delta Diversion intakes (fig. 1).

Fish Tagging and Transport

Juvenile, late-fall run Chinook salmon reared at the U.S. Fish and Wildlife Service Coleman 

National Fish Hatchery in Anderson, California, were obtained for this study. Fish were held at the 

hatchery until just prior to tagging, when they were transported to the tagging facility at the Sutter 

Mutual Water Company pumping facility in Robbins, California, at the Tisdale Weir on the 

Sacramento River, approximately 57 rkms upstream of the Fremont Weir. Each fish was anaesthetized, 

individually weighed and measured, and surgically implanted with an acoustic transmitter (Vemco, 

Ltd.; Model V5). Fish were screened and selected for tagging only if their weight exceeded 13 g so 

that anticipated tag burden would be less than 5 percent. After being allowed to recover from surgery 

in river water supersaturated with oxygen for at least 10 minutes, tagged fish were held without further 

handling for 15–38 hours and then were transported for release. Measurements of tagged and released 

fish ranged from 108 to 218 mm in fork length and from 13.4 to 116.8 g in weight, with means of 

165.3 mm and 50.0 g. Tagging and transport procedures are further detailed by Liedtke and Hurst 

(2017). 
5 

Figure 1. Map showing study area, Sacramento-San Joaquin River Delta, California. (Telemetry stations used for 

Delta-wide estimates are labeled with dots. The four telemetry stations which bracket the three proposed North 

Delta Diversion (NDD) intakes and were used to estimate NDD intake area survival were not used in the Deltawide survival model. Place names are included for reference. The Yolo Bypass, indicated by the shaded polygon, 

is only sometimes flooded.) 
6 

Fish Release Strategy

A major objective of this study was characterizing fish behavior at the Fremont Weir and 

utilization of the Yolo Bypass over a wide range of hydrologic variability. These conditions include 

river flows insufficient to overtop the Fremont Weir as well as the ascending limb, peak, and 

descending limb of flood pulse discharges sufficient to cause overtopping of Fremont Weir and inflow 

into the Yolo Bypass. As such, planning fish-release timing and location was approached with an 

adaptive management strategy. These decisions were made by a small team of agency representatives 

knowledgeable in either the hydraulics of the Sacramento River/Sutter/Yolo Bypass system during 

high flows or in the movements of juvenile salmon in this region. Release timing was determined by 

monitoring the weather, hydrologic forecasts, and discharge data collected in the upper Sacramento 

River basin. 

Five releases were conducted, for a total of 1,197 tagged fish released (table 1). The first two 

releases of 240 tagged fish occurred during flows insufficient to overtop the Fremont Weir and were 

intended primarily to document the distribution of fish as they passed Fremont Weir. These releases 

were focused on attempting to determine the effect of secondary circulation in concentrating fish 

density on the outside of bends (Blake and others, 2017). In this study phase, we targeted stages of 18–

25 ft NAVD88 during the ascending limb of the hydrograph, but prior to flow into the Yolo Bypass 

over the Fremont Weir. These stages were reflective of potential periods in which a notch could 

operate based on design considerations at the time of the study. 

Table 1. Dates and numbers of acoustically tagged juvenile Chinook salmon released, Sacramento-San Joaquin 

River Delta, California. 

Release 

group Date(s)

Number 

released 

at Tisdale

Number 

released 

into Yolo 

Bypass

Number 

released 

at Verona

1 February 21 240 0 0

2 March 6 240 0 0

3 March 11–12 141 99 0

4 March 15–16 40 100 100

5 March 17–18 40 98 99

The final three releases of approximately 240 tagged fish were conducted to study passage in 

the Yolo Bypass during: (1) initial over topping, (2) peak flow into the Bypass, and (3) descending 

limb of bypass flooding (fig. 2). During periods when the Fremont Weir was overtopped (Release 

Groups 4 and 5), we released approximately 40 study fish upstream of the Fremont Weir at Tisdale 

Weir to determine rates of entrainment into the bypass. Approximately 100 fish were released directly 

into the Yolo Bypass as close as possible to the Fremont Weir and 100 fish into the Sacramento River 

just downstream of the Fremont Weir to assure an adequate sample size for downstream receivers in 

both the Yolo Bypass and in the North Delta survival arrays, regardless of entrainment rate into the 

bypass (table 1). Fish released into the Yolo Bypass during Release Group 3 were released into the 

Tule Canal just upstream of I-5 since the Fremont Weir had not yet overtopped and flows were too low 

within the Yolo Bypass just downstream of the weir (fig. 1). Each release was timed to distribute 

released fish as evenly as possible over a single 24-hour period as they passed downstream of the 

Fremont Weir. For example, for a release group in which fish were released at Tisdale Weir, Fremont 

Weir, and into the Yolo Bypass, there was a delay between the Tisdale release and the other release 

sites as to allow the upstream-released fish time to migrate to the Fremont Weir. In this way, all fish 

within a release group would to a large extent experience similar hydrologic conditions. 
7 

Figure 2. Instantaneous river flows in Yolo Bypass (red), in the Sacramento River at Freeport (dark blue), and in 

Cache Slough (light blue) taken at 15-minute intervals, with times of release (pink) for each of five release groups.

(ft3/s, cubic foot per second)

Data Processing

Data downloaded from the Vemco acoustic telemetry receivers consisted of individual detected 

pulses, uniquely identifiable by tag. Data were post-processed and filtered into a form suitable for 

subsequent analyses. 

Screening and Removal of False Positive Detections 

Acoustic receivers are susceptible to interpreting ambient or mechanical acoustical noise as tag 

detections. In the case of Vemco receivers, individual pulses recorded by the datalogger have a small 

chance of not having originated from the designated tag. These false positive detections were screened 

from the data by requiring at least two independent pulses from a given tag at the same location within 

a 30-minute period in order to be considered a valid detection. Single pulses not meeting these criteria 

were filtered from the data and disregarded in further analyses.

Screening and Removal of Detections of Predated Tags 

Mark-recapture analysis relies on the assumption that detections represent live, tagged 

individuals. As such, it is critical to screen for and remove detections of tags implanted in juvenile 

salmon smolts which may have been eaten by piscivorous predators, since treating these detections as 

having originated from live smolts would result in positively biased survival estimates.

Detections of tags that may have been consumed by predators were identified and removed 

from the data set by hierarchical cluster analysis following the adapted methods of Gibson and others 

(2015) as reported in California Department of Water Resources (2016). This process consisted of 

several steps involving application of clustering to several movement metrics, identification of clusters 

with evidence of predation, and review of detection histories to identify when suspected predation 

occurred. Detections of tags from known predators were included within the cluster analyses, which 
8 

allowed examination of how movements of known predatory fishes were grouped with putative 

predators of tagged juvenile Chinook salmon. 

The metrics selected for use in the hierarchical cluster analysis were as follows: 

1. Total elapsed time between first detection after release and last detection, in days (ArrayTime); 

2. Number of consecutive detection events occurring at the same location (NSame); 

3. Total distance travelled divided by the total number of days spent in the array (PathDays); and 

4. Number of transitions that were deemed to be only possible by a predator (that is, movement 

upstream against the flow) (NPred). 

ArrayTime was calculated by subtracting the time of first detection after a tag was released 

from the time of last detection for that tag. NSame was calculated as the total number of detection 

events from a single tag that occurred at the same site consecutively. PathDays was estimated by 

summing the total distance travelled within the array and dividing the distance by the total time the 

fish was in the array (release time to last detection time). NPred was calculated by summing the 

number of predator-like transitions that occurred in a detection history. Predator-like transitions were 

defined as upstream movements between telemetry locations that could only have occurred by fish 

swimming against downstream river flow, which would be extremely unlikely behavior for juvenile 

Chinook salmon. All metrics were standardized to have a mean of zero and a standard deviation of 

one. 

The h-clust package in R was used to create a dendrogram of all the tags from the results of 

hierarchical clustering, based on Ward’s minimum variance method (Ward, 1963; Gibson and others, 

2015). Using the dendrogram, the tags were divided into three groups, and then the group with most of

the known predator tags was selected for further scrutiny. Any juvenile Chinook salmon tag that was 

assigned to this group was considered to exhibit behavioral patterns consistent with that of predators.

Although this approach identified putative predators, it did not identify the point in the detection 

history at which the juvenile Chinook salmon was consumed. Therefore, all detection histories of 

juvenile Chinook salmon tags that were grouped with predators were manually examined to identify 

the point in the detection history where the tag transitioned from juvenile Chinook salmon- to 

predator-like behavior. 

Screening of the detection data for potential predator detections via hierarchical cluster analysis 

resulted in 220 tag detection records flagged for review. All known predator tags with more than a 

single detection event fell into the same group as the smolt tags flagged for review. Manual review of 

each of the detection histories resulted in 16 tags determined to have been predated during the time 

each was active in the acoustic array. All 16 tag detection histories were truncated at the point we 

determined the tag had been predated, and subsequent detections were censored from further analysis. 

Survival, Routing, and Travel-Time Analysis 

Multistate Mark-Recapture Survival Model

We designed a statistical model to estimate reach- and route-specific survival for primary 

outmigration routes through the Delta (fig. 3). We used the general framework of multistate markrecapture modelling to estimate the parameters of interest (Lebreton and others, 2009). Here, the term 

“state” refers to the fact that juvenile salmon migrating through the Delta do so through one or more 

routes. Fish can transition between these routes at discrete junctions, and their survival is dependent on 

which route they take to traverse the study area. Routes include the Sacramento River (Route A), Yolo 

Bypass (Route B), Sutter and Steamboat sloughs (Route C), and the Interior Delta via Georgiana 

Slough (Route D). Hydrophone monitoring locations were selected so that survival within these four 

routes was estimable (fig. 1). 
9 

Figure 3. Schematic of the multistate mark-recapture model with parameters indexed by state (migration route) 

and sampling occasion. (Parameters include reach-specific survival probabilities [S], site-specific detection 

probabilities [P], routing probabilities [ψ ], and λ , the joint probability of surviving and being detected at telemetry 

stations downstream of site A6. Release locations are indicated [g]). 
10 

The mark-recapture model that is shown in fig. 3 estimates the following three types of 

parameters from detections of tagged juvenile Chinook salmon: 

S jt Survival Probability, defined as the probability of surviving from telemetry station t-1 

within route j to telemetry station t (that is, to the next downstream telemetry station);

ψ jt Route Entrainment Probability, defined as the probability of entering route j at occasion

t, conditional on surviving to occasion t; and 

Pjt Detection Probability, defined as the probability of detecting a tagged fish at telemetry 

station t within route j, conditional on fish and tags surviving to telemetry station jt. 

All parameters were estimated independently for each of the five releases described earlier.

Subscripting by release is omitted throughout this section for ease of reading. While most survival 

probabilities used in our model represent survival within a given reach of a single channel, some 

survival parameters represent the average survival of fish migrating through several possible 

unmonitored channels. For example, SSCC4 (fig. 3) represents the average survival of fish migrating 

through the combination of Sutter, Steamboat, and Miner Sloughs, weighted by the unknown number 

of fish using each possible route. 

To estimate these parameters, telemetry data first were summarized into alpha-numeric codes 

called a “capture history” that compactly represented each fish’s movement history through the 

telemetry network by indicating detections at each telemetry station. In the case of the model shown in 

fig. 3, each capture history would be seven digits/letters long, one for each sampling occasion. Each 

individual letter represents detection within a specific route at that sampling occasion, with a 0 

denoting no detection. As an example, consider the capture history “AA00DAA.” This tag would have 

been detected in Route A on sampling occasions 1 and 2, not detected on sampling occasions 3 and 4, 

detected in Route D on sampling occasion 5, and in Route A again on sampling occasions 6 and 7 

(figs. 1, 3). Of note in this example is that migration routing can sometimes be inferred even when fish 

were not detected; here we know that the fish remained in the Sacramento River at the junction with 

Sutter and Steamboat Sloughs, and subsequently migrated through Georgiana Slough into the Interior 

Delta, since it was detected at location D5 at the base of the Mokelumne River.

Each capture history is viewed as one possible outcome from a multinomial distribution and 

has an associated probability of occurrence defined as a function of the model parameters. This 

likelihood function has the form: 

( ,, , ) nm

m m

m M

L S PRn ψ π ∈

∝ ∏ (1) 

where M is the set of all possible capture histories;

R is the number of fish released;

mn is the number of fish with capture history m ; and 

π m is the multinomial cell probability for capture history m , defined in terms of 

parameters ψ , , S P . 
11 

The equation for π m is:

m

m

m mt

L

m jt jt jt L

t F j J

π ψ θχ S = ∈

= ∏ ∑ × , (2) 

where mt J is the set of possible routes available at occasion t given capture history m ; 

Fm is the occasion of first possible detection after release for capture history m ; 

Lm is the occasion of last detection for capture history m ; 

θ jt represents Pjt for route j and occasion t if capture history m indicates detection in 

route j and occasion t , and represents 1− Pjt otherwise; and 

Lm χ represents the probability of not being detected after occasion m t L = . 

The parameter χt is defined recursively (Cormack, 1964); 1 χ T = for the final occasion T (here, T=7, 

downstream from Chipps Island) since there are no opportunities to detect fish after the final occasion, 

and 

1 ( ( ) ( ) 1 1 ) ntt t j jt jt jt

j J

χχ ψ SP S +

∈

= × − +− ∑ (3) 

for occasions t T ∈ − { } 1, , 1  . 

Travel Time Likelihood

For each tagged fish, the time of release and each subsequent time of detection was recorded.

These recorded detection times were converted so that each detection provided the time elapsed since 

the previous detection. Recalling the previous example capture history “AA00DAA,” travel time data 

consists of five elapsed travel times, associated with each of the five detections in the capture history.

The first time represents time elapsed from release to first detection at telemetry station A1 in this 

example. When one or more consecutive detections are missed, the next detection is associated with 

the cumulative elapsed time over multiple reaches since the last prior detection. In our example, the 

time associated with the detection “D” in the fifth digit represents elapsed time from detection at A2 to 

detection at D5. 

These elapsed travel time data were analyzed to estimate independent travel time parameters 

for each adjacent pair of release/acoustic telemetry locations. For each reach, travel times were 

modeled as arising from a gamma distribution. Thus, for a reach in route j from occasion t to occasion 

t+1, the likelihood of the recorded elapsed travel time between these two stations is defined by the 

following equation: 

( ) 1 , jt it L e jt it it

α βτ α βτ τ − − ∝ , (4) 

where it τ is the recorded travel time for individual i from occasion t to occasion t+1.
12 

While this approach of estimating travel time parameters for individual reaches defined by 

adjacent telemetry stations produces unbiased estimates, the model by itself does not make use of all 

the information in the recorded data. When detections are missing, there is no data available for that 

individual to directly model travel times for the reaches immediately upstream and downstream of the 

missing detection since we do not know when that fish arrived. However, using a property of the 

gamma distribution, namely that the sum of gamma distributed random variables is itself gamma

distributed when each of the random variables has the same parameter β , we can indirectly 

parameterize partially missing travel time data. In our example, we have recorded time elapsed from 

station A2 to D5. This represents the sum of the times from A2 to A3, A3 to D4, and D4 to D5. The 

sum of gammas property then results in the ability to easily model elapsed travel times between nonadjacent telemetry stations. The overall travel time likelihood is therefore: 

( ) ( )

1

, , ,

i it

R

jt jt

i t j J

L R gamma τ

αβ τ ψ α β = ∈ ∈

∝ × ∏∏ ∑ , (5) 

where i τ is the set of recorded travel time pairs for individual i; 

it J is the set of all routes available for individual travel time pair it τ ; and 

gamma(α,β) is the pdf of a gamma random variable detailed in eq. 1.4. 

Derived Parameters

Fundamental parameters were estimated under this likelihood at the reach scale (that is, over 

the region bounded by adjacent telemetry stations). However, other parameters of interest are on a 

different spatial scale as these fundamental reach-specific parameters. For example, route-specific 

survival is defined as total overall survival from the release point at Tisdale downstream to Chipps 

Island for fish traversing a specific route which generally encompasses multiple reaches. This routespecific survival is defined as the product of individual reach-specific survival parameters that 

comprise the route. Likewise, the probability of migrating through a specific route is not the same as 

that of initially entering the route if there are multiple junctions within that route. This overall route 

entrainment probability is defined as the product of the entrainment probabilities for each junction 

along that route. Overall Delta-wide survival from release at Tisdale to Chipps Island can be calculated 

as the sum of the route-specific survival probabilities, weighted by the route entrainment probabilities. 

Since we wish to compare survival through the Yolo Bypass to survival for all other routes, we can 

similarly calculate non-Yolo Bypass survival, omitting route entrainment and route-specific survival 

for the Yolo Bypass route from this calculation. Finally, we also calculate a daily survival for fish 

migrating via each major route, as well as for fish migrating via any of the non-Yolo Bypass routes. 

Daily survival is calculated by taking the Routej E   τ

  th root of survival for a given route from the 

Fremont Weir to Chipps Island, where Routej E   τ

  is the expected travel time for Routej in days. 
13 

Specifically,

 Routej S represents survival from the Fremont Weir to Chipps Island for Routej, 

and is calculated by taking the product of reach-specific survivals that trace a 

unique migration route through the Delta; 

 

 

 

Routej ψ represents overall entrainment probability for Routej, and is calculated by 

taking the product of junction-specific entrainment probabilities along that route; 

{ } , , j j non Yolo Route Route

j AC D

S S − ψ ∈= ∑ represents non-Yolo overall survival; 

1 /

T

jt

t

Route Route j j SD S

β

α

=

∑ = represents daily survival for fish migrating via Routej; and 

{ } , ,

/ / j j non Yolo Route Route

j AC D

S D − ψ S D ∈

= ∑ represents non-Yolo daily survival; 

where J ABCD ∈{ } ,,, is one of the possible routes through the Delta from the Fremont Weir to Chipps

Island, and the Yolo Bypass is part of RouteB. 

Bayesian Estimation via Hamiltonian Monte Carlo

All parameters were estimated simultaneously using Hamiltonian Monte Carlo (HMC) methods 

using the Stan modeling software package (Carpenter and others, 2017). The observed travel times and 

capture history of each tagged individual comprised all data whose total likelihood was expressed as 

the product of the survival and travel time likelihoods described above. Standard normal prior 

distributions were placed on the transformed travel time parameters log( ) α β jt , and all other 

parameters were given default implicit priors by the Stan software. Four separate HMC chains were 

run in Stan for 2,000 iterations each, discarding the first 1,000 as burn-in. Posterior samples were 

checked for convergence and mixing, and the resulting sample of 4,000 draws was then reported via 

median, 5th and 95th percentiles for each parameter estimated. Derived parameters were calculated by 

creating a new posterior sample for each derived parameter. This was achieved by using the formula 

for a derived parameter across each of the 4,000 sample draws. The medians and credible intervals 

reported for these derived parameters are thus the corresponding quantiles of these derived posterior 

samples.

Spatial Distribution and Survival Within the Yolo Bypass

The cross-stream distribution of acoustic-tagged fish in the Yolo Bypass was estimated at the 

point where I-80 crosses the bypass just west of the city of Sacramento. A total of 19 hydroacoustic 

receivers were deployed on the south side of two sections of roadway bridging the bypass, separated 

by an island (fig. 1). The location of each fish in the bypass was defined as the distance in meters from 

the I-80 bridge receiver at the eastern most end of the array to the receiver where the fish was first 

detected. The first group of receivers monitoring the east bridge section was comprised of 15 receivers 

ranging from 0 to 2,559 m from the east bank of the bypass. The second group of four receivers on the 

west bridge section ranged from 4,231 to 4,812 m distant. The receivers within both groups were 

generally about 200 m apart, but in a few cases were more closely spaced. A Gaussian kernel density 

function was applied to the data using R to estimate the horizontal density of fish across the bypass (R 

Core Team, 2015). Individual density distributions were generated for fish released at each of the 
14 

Tisdale, Fremont Weir, and Tule canal release sites, because the proximity of each release site to the I80 detection array (range 12.5–77.7 km) might potentially influence the horizontal distribution of fish 

in the bypass. 

Additionally, we investigated whether evidence existed for differences in survival in the Yolo 

Bypass as a function of east-to-west spatial location. For this analysis, a Cormack-Jolly-Seber (CJS) 

mark-recapture model was fit to the data (Cormack, 1964; Jolly, 1965; Seber, 1965) to estimate 

survival within the Yolo Bypass from the I-80 bridge downstream to the detection station at Cache 

Slough. Each fish’s cross-stream position at the I-80 bridge was used as an individual covariate on 

survival to quantify the magnitude of an east-west gradient in survival. 

California WaterFix North Delta Diversion Intake Study

To provide baseline information against which future effects of the intakes on juvenile salmon 

survival can be measured, survival probabilities were estimated for three Sacramento River reaches 

containing the proposed sites of the three new North Delta Diversion intake structures. The three 

reaches were 3.23, 4.12, and 5.37-km-long, respectively (fig. 1). Survival probabilities were estimated 

independently for each of the five fish releases. Of the 1,197 tagged fish released for this study, only 

fish that were detected at the array in the Sacramento River below the mouth of the Feather River were 

included as part of the analysis. 

A CJS mark-recapture model was used to estimate the reach survival and detection probability 

parameters for the three reaches (Cormack, 1964; Jolly, 1965; Seber, 1965). Additionally, cumulative 

and standardized reach survival probabilities were calculated as derived model parameters. The 

cumulative survival probability for the combined total reach length (12.72 km) was calculated as the 

product of the three individual reach survival parameters. As with the multistate model, model 

parameters were estimated using HMC within the Stan probabilistic modeling language. Prior 

distributions for the model parameters were assumed to be uniform between 0 and 1. A total of 40,000 

simulated post-warm up samples were obtained from the Bayesian posterior distribution using four 

independent Markov chain Monte Carlo chains. From these samples the median (50th percentile) 

survival and detection probabilities, and the 95-percent credible intervals (2.5 to 97.5 percentile) were 

determined. 

Results

Survival, Routing, and Travel Time

Survival Estimates

Overall survival through the Delta from Fremont Weir to Chipps Island varied by route, with 

estimates ranging from 0.142 to 0.843 (table 2; fig. 4). Survival was generally highest for fish 

remaining in the mainstem Sacramento, with release specific survival estimates ranging from 0.552 to 

0.843, and with survival for three of the five release groups above 0.7. Survival among routes was 

lowest for fish migrating through the Interior Delta via Georgiana Slough; release specific survival 

estimates for this route ranged from 0.142 to 0.695, with survival for three of the five release groups 

lower than 0.6. Survival estimates for all routes except for the Yolo Bypass varied by release group in 

a similar manner: later release groups, coincident with greater flow and overtopping of the Fremont 

Weir, displayed higher survival estimates than did earlier release groups. For the three release groups 

where survival from the Fremont Weir to Chipps Island through the Yolo Bypass was estimable, those 

estimates were quite consistent, ranging from 0.659 to 0.689. 
15 

Table 2. Derived parameters for route-specific overall survival from the Fremont Weir to Chipps Island, 

Sacramento-San Joaquin River Delta, California. 

[Lower and Upper credible limit: Denotes the 5th and 95th percentiles of the posterior distributions for each parameter, 

respectively] 

Name Release Median

Lower

credible

limit

Upper 

credible 

limit

Route description

Survival parameters

SSAC 1 0.552 0.458 0.644 Sacramento River 

2 0.685 0.549 0.832

3 0.704 0.549 0.867

4 0.748 0.634 0.860

5 0.843 0.738 0.925

SYOLO 3 0.689 0.558 0.820 Yolo Bypass to Cache 

4 0.677 0.597 0.767 Slough

5 0.659 0.574 0.745

SSUT/STM 1 0.369 0.276 0.473 Sutter Slough or Steamboat 

2 0.654 0.524 0.781 Slough

3 0.614 0.467 0.761

4 0.697 0.531 0.827

5 0.716 0.580 0.836

SGEO 1 0.142 0.068 0.256 Georgiana Slough to 

2 0.385 0.252 0.548 Interior Delta

3 0.564 0.390 0.760

4 0.695 0.526 0.838

5 0.613 0.466 0.760

SNON-YOLO 1 0.352 0.291 0.419 All routes combined except 

2 0.507 0.413 0.616 Yolo Bypass

3 0.600 0.490 0.713

4 0.665 0.564 0.762

5 0.735 0.652 0.811
16 

Figure 4. Median probability of survival with upper and lower credible limits (the 5th and 95th percentiles of the 

posterior distributions for each parameter, respectively) from Fremont Weir to Chipps Island by route through the 

North Delta, California. 

Parameter estimates of survival within individual reaches ranged from 0.375 to 0.992 

(appendix 1; table 1). Among reaches, survival was generally highest in upstream, riverine reaches, 

including the Sacramento River above the entrance to Georgiana Slough (reaches A2, A3, A4, and 

A5), the upper Yolo Bypass from Fremont Weir to the I-80 bridge (reach B1), and Steamboat Slough 

(reaches C41B and C42B). Survival was generally lowest in tidal reaches such as the Interior Delta 

from the junction of Georgiana Slough with the Lower Mokelumne River to Chipps Island (reach D6), 

and from the junction of Cache Slough with the Sacramento River to Chipps Island (reach C6). Among 

releases, reach-specific survival estimates displayed similar trends to those noted for route-specific 

survival, with Release Groups 1 and 2 coinciding with lower flows before overtopping of the Fremont 

Weir associated with lower survival than in Release Groups 3, 4, and 5 when flows were higher. 
17 

Migration Routing Estimates

We estimated the proportion of juvenile salmon migrating from the Fremont Weir to Chipps 

Island via each of the four main routes. Median estimates of the proportion migrating via the 

Sacramento River varied by release group and ranged from 0.115 to 0.501 (table 3). For Release 

Groups 3 through 5, estimates of the proportion migrating through the Yolo Bypass ranged from 0.012 

to 0.801. Migration proportions through Sutter and Steamboat Sloughs and Georgiana Slough to the 

Interior Delta were generally lower, with estimates for the proportion migrating via Sutter and 

Steamboat Sloughs ranging from 0.050 to 0.361, and via Georgiana Slough and the Interior Delta 

ranging from 0.031 to 0.233 (table 3).

Table 3. Derived parameters for route-specific entrainment probabilities from the Fremont Weir to Chipps Island, 

Sacramento-San Joaquin River Delta, California. 

[Lower and Upper credible limit: Denote the 5th and 95th percentiles of the posterior distributions for each parameter, 

respectively] 

Name Release Median

Lower 

credible

limit

Upper credible

limit Route description

Routing parameters

ΨSAC 1 0.501 0.434 0.567 Sacramento River 

2 0.447 0.389 0.505

3 0.389 0.321 0.461

4 0.115 0.061 0.187

5 0.458 0.371 0.543

ΨYOLO 1 0.000 0.000 0.000 Yolo Bypass to Cache 

2 0.000 0.000 0.000 Slough

3 0.012 0.003 0.035

4 0.801 0.687 0.890

5 0.040 0.008 0.113

ΨSUT/STM 1 0.311 0.252 0.375 Sutter Slough or Steamboat 

2 0.360 0.303 0.420 Slough

3 0.361 0.292 0.435

4 0.050 0.025 0.093

5 0.294 0.216 0.381

ΨGEO 1 0.186 0.137 0.242 Georgiana Slough to 

2 0.191 0.148 0.239 Interior Delta

3 0.233 0.175 0.297

4 0.031 0.015 0.054

5 0.198 0.147 0.254

ΨNON-YOLO 1 1.000 1.000 1.000 All routes combined except 

Yolo Bypass

2 1.000 1.000 1.000

3 0.988 0.965 0.997

4 0.199 0.110 0.313

5 0.960 0.887 0.992
18 

Route migration proportions for Release Group 4, when both flows and the river stage at 

Fremont Weir were highest, contrasted greatly with migration proportions for the other four release 

groups. Median entrainment probability into the Yolo Bypass for Release Group 4 was estimated to be 

greater than 80 percent. This proportion coincides with the lowest estimates of migration proportion 

for each of the other routes and was the only release group of the three where fish had an opportunity 

to migrate through the Yolo Bypass where more than 5 percent of fish were estimated to have done so. 

For each of the other release groups, when few fish were estimated to have migrated through the Yolo 

Bypass, migration proportions through each of the other three routes was quite stable (fig. 5).

Figure 5. Median probability of entrainment with upper and lower credible limits (the 5th and 95th percentiles of 

the posterior distributions for each parameter, respectively) from Fremont Weir to Chipps Island, California, by 

route. 
19 

Travel Time Parameter Estimates 

Mean travel time estimates varied by route through the Delta and by release group, with 

estimated mean travel time from the Fremont Weir to Chipps Island ranging from 2.70 days to 8.06 

days (fig. 6). Travel time for non-Yolo Bypass routes was shorter during Release Groups 3, 4, and 5, 

when flows were higher and the Fremont Weir was overtopping, than for Release Groups 1 and 2 

(table 4; fig. 6). For fish migrating via the Yolo Bypass, travel time did not vary substantially with 

release group. For all release groups, fish migrating via either the mainstem Sacramento River (mean 

travel time range 2.70–6.74 days) or Sutter and Steamboat Sloughs (range 2.71–7.04 days) arrived at 

Chipps Island faster than fish migrating via the Yolo Bypass (predicted mean travel time range 4.19–

5.08 days for Release Groups 3–5). Fish migrating via the Interior Delta exhibited the longest 

estimated mean travel times (range 5.41–8.06 days). 

Table 4. Derived parameters for route-specific travel times from the Fremont Weir to Chipps Island, SacramentoSan Joaquin River Delta, California. 

[Lower and Upper credible limit: Denote the 5th and 95th percentiles of the posterior distributions for each parameter, 

respectively] 

Name Release Median

Lower 

credible

limit

Upper 

credible

limit

Route description

Predicted mean travel time

τττSAC 1 6.743 6.404 7.090 Sacramento River 

2 3.669 3.480 3.859

3 3.163 2.936 3.393

4 2.696 2.457 2.942

5 2.945 2.732 3.169

τττYOLO 3 4.186 4.001 4.381 Yolo Bypass to Cache 

4 5.084 4.827 5.361 Slough

5 4.531 4.294 4.785

τττSUT/STM 1 7.040 6.374 8.009 Sutter Slough or Steamboat 

2 4.308 3.936 4.891 Slough

3 2.885 2.659 3.127

4 2.792 2.376 3.443

5 2.712 2.465 2.983

τττGEO 1 8.055 6.993 9.239 Georgiana Slough to 

2 7.512 6.888 8.134 Interior Delta

3 5.608 5.158 6.073

4 6.401 5.694 7.148

5 5.405 4.933 5.890
20 

Figure 6. Route-specific travel time quantiles from Fremont Weir to Chipps Island, Sacramento-San Joaquin 

River Delta, California. (Dots indicate medians, thick lines show 25th–75th percentiles, and ends of thin lines 

show 5th and 95th percentiles. Travel time quantiles are derived from a gamma(α β, ) distribution where α β,

are the median posterior values.) 
21 

Mean Daily Survival Probabilities

Derived per day survival estimates as calculated according to the definitions given in the 

Derived Parameters subsection of the Methods above were generally consistent across both route and 

release group. Mean daily survival estimates ranged from 0.785 to 0.945 (table 5). Daily survival was 

lowest for the earlier release groups in the Sutter and Steamboat Slough and Interior Delta routes, 

when flows were lower. Daily survival in the Yolo Bypass route was similar to that in the mainstem 

Sacramento River for Release Groups 3 through 5, when the Fremont Weir was overtopping, and was 

not substantially different from combined weighted daily survival through non-Yolo routes. 

Table 5. Derived parameters for route-specific daily survival from the Fremont Weir to Chipps Island, 

Sacramento-San Joaquin River Delta, California. 

[Lower and Upper credible limit: Denote the 5th and 95th percentiles of the posterior distributions for each parameter, 

respectively] 

Name Release Median

Lower 

credible

limit

Upper 

credible

limit

Route description

Daily survival parameters

S/DSAC 1 0.916 0.890 0.937 Sacramento River 

2 0.901 0.848 0.952

3 0.895 0.826 0.956

4 0.898 0.843 0.946

5 0.944 0.902 0.974

S/DYOLO 3 0.915 0.870 0.953 Yolo Bypass to Cache 

4 0.926 0.903 0.949 Slough

5 0.912 0.883 0.937

S/DSUT/STM 1 0.869 0.832 0.900 Sutter Slough or Steamboat 

2 0.907 0.859 0.944 Slough

3 0.844 0.768 0.910

4 0.880 0.794 0.935

5 0.884 0.815 0.937

S/DGEO 1 0.785 0.711 0.847 Georgiana Slough to 

2 0.881 0.831 0.923 Interior Delta

3 0.903 0.844 0.952

4 0.945 0.904 0.973

5 0.914 0.866 0.951

S/DNON-YO 1 0.885 0.862 0.905 All routes combined except 

2 0.901 0.865 0.934 Yolo Bypass

3 0.884 0.836 0.927

4 0.907 0.873 0.938

5 0.920 0.891 0.945
22 

Spatial Distribution and Survival within the Yolo Bypass

The horizontal distribution of tagged fish from east to west in Yolo Bypass parallel to I-80 

tended to be increasingly skewed towards the east bank the closer the fish’s release site was to I-80 

(fig. 7). This likely reflects not only the proximity of a particular release site to the I-80 detection 

array, but also the point where the fish were released, particularly those fish released within the 

bypass, as both the Fremont Weir and Tule Canal releases occurred within the bypass near the east 

bank. The horizontal density of fish released closest to the I-80 array at the Tule Canal was greatly 

skewed towards the east bank. The densities of these fish dropped off rapidly with distance from the 

east bank out to about 370 m and remained low to a maximum distance of about 2,000 m. Fish 

released in the bypass below the Fremont Weir also had a horizontal distribution skewed towards the 

east bank of the bypass, but it was much less pronounced and densities were only about a third of those 

of the Tule Canal fish near the east bank. Fish densities for this group peaked about 140 m from the 

east end of the array, decreased slowly to about 670 m and remained steady out to about 1,280 m, and 

then declined again down to the lowest densities between 2,000 and 2,500 m from the east bank. 

In contrast to within-Yolo release groups, the fish that were released in the Sacramento River 

upstream of Fremont Weir and that entered the bypass volitionally were nearly equally dispersed from 

0 to about 2,000 m from the east bank before densities gradually decreased out to 2,500 m (fig. 7). No 

fish were first detected on the western group of four receivers located 4,231 to 4,812 m from the east 

bank; however, it is important to note that since the Yolo Bypass is a seasonally inundated floodplain 

and not a well-defined river channel, this far western extent of the Bypass may not have been flooded 

for parts of the study duration. 

Median survival for all tagged fish detected at the I-80 array to Cache Slough was estimated at 

0.839 (5 and 95 percent credible limits 0.784 and 0.887, respectively). Survival did not vary 

significantly with location of first detection within the I-80 array, and no effect of distance of first 

detection from the east bank on survival was observed. For example, survival from I-80 to Cache 

Slough for a fish first detected at the easternmost receiver of the I-80 array was estimated at 0.847 

(0.784, 0.901 credible interval), while fish first detected at the westernmost receiver had an estimated 

survival of 0.819 (0.690, 0.919 credible interval). 
23 

Figure 7. Cross-stream distribution of tagged fish distribution within Yolo Bypass at the I-80 bridge, separated by 

release site, California. 
24 

California WaterFix North Delta Diversion Intake Study

The number of fish used to estimate juvenile Chinook salmon survival within the three 

contiguous Sacramento River reaches encompassing proposed North Delta Diversion intake sites 

ranged from 81 to 240 among the five fish releases (table 6).

Table 6. Number of juvenile Chinook salmon used to estimate survival for three Sacramento River reaches

encompassing proposed North Delta Diversion intakes in the North Delta, Sacramento-San Joaquin River Delta, 

California. 

Number of fish by release

Release site 1 2 3 4 5 Total

Tisdale 240 240 81 5 28 594

Verona 0 0 0 100 99 199

Total 240 240 81 105 127 793

Median absolute reach survival probabilities for the three Sacramento River reaches 

encompassing the three proposed North Delta Diversion intake sites were generally high among all 

five fish releases (range 0.975–0.995; table 7). Differences in median survival among releases within a 

reach were 0.020 or less (range 0.013–0.02). Median cumulative survival probabilities for the 

combined 12.72 kilometer reach generally ranged between 0.921 and 0.942, except for the second fish 

release where the median cumulative survival was 0.974 (table 7). Median survival probabilities were 

consistently higher for the second release than for the other releases for all three reaches (range 0.990–

0.995). Differences in median reach survivals within releases were within the range of parameter 

uncertainty indicated by the 95 percent credible intervals for each parameter.

Table 7. Median reach-specific and cumulative survival estimates, and 95-percent credible intervals by fish

release and reach for the three proposed water-intake sites, Sacramento-San Joaquin River Delta, California. 

Absolute reach survival

Release Reach 1 Reach 2 Reach 3 Cumulative survival

1 0.984 (0.957–0.996) 0.984 (0.956–0.997) 0.977 (0.946–0.993) 0.942 (0.900–0.971)

2 0.994 (0.967–1.000) 0.990 (0.962–0.999) 0.995 (0.975–1.000) 0.974 (0.937–0.993)

3 0.980 (0.916–0.999) 0.981 (0.917–0.999) 0.984 (0.924–0.999) 0.932 (0.855–0.981)

4 0.976 (0.903–0.999) 0.977 (0.907–0.999) 0.983 (0.922–0.999) 0.921 (0.844–0.977)

5 0.987 (0.945–1.000) 0.988 (0.945–1.000) 0.975 (0.921–0.999) 0.942 (0.882–0.982)

Mean 0.984 0.984 0.983 0.942
25 

Discussion

In release groups where survival in the Yolo Bypass was estimable, overall survival from the 

Fremont Weir to Chipps Island was similar between fish travelling through the Yolo Bypass and fish 

travelling non-Yolo routes (fig. 4). Upon closer inspection, however, interesting patterns in survival 

emerge. Survival of migrating juvenile Chinook through the North Delta has been found to exhibit a 

positive relationship with flow in routes other than the Yolo Bypass (Kjelson and others, 1982; Kjelson 

and Brandes, 1989; Newman and Rice, 2002; Newman, 2003; Perry and others, in press). Although we 

did not conduct an analysis that relates survival directly to flow covariates, figure 4 shows that in nonYolo routes, survival increased with each successive release, coincident with an increase in flow 

among releases (fig. 2).

The pattern of higher survival coincident with higher flows seen in non-Yolo Bypass routes 

was not apparent in the Yolo Bypass route survival estimates, which were remarkably consistent 

across the three release groups for which estimates are available (fig. 4). This consistency holds even 

for Release Group 3, during which the Fremont Weir had not quite overtopped, and for which tagged 

fish were released directly into the Yolo Bypass. Examination of detection times at Cache Slough 

reveals that a large majority of these fish exited the Yolo Bypass 1–3 days after initial overtopping of 

the Fremont Weir. Thus, there is a strong possibility that while flows on release in the Yolo Bypass 

were quite low for this group, subsequent overtopping of the Fremont Weir could have led to increased 

flows, shorter travel times, and high survival (fig. 2). 

While differences in survival between Yolo and non-Yolo routes were small at the high flows 

seen during this study, at lower flows, survival through non-Yolo Bypass routes has been shown to 

decrease. Survival was lower through these routes for Release Groups 1 and 2 when no fish migrated 

through the Yolo Bypass (fig. 4). If survival through the Yolo Bypass is indeed largely independent of 

flows in the Bypass, it seems possible that overall salmon survival could benefit by diverting fish into 

the Yolo Bypass when flows through the North Delta are lower, provided flows in Yolo were at least 

as high as during Release Group 3. A strategically placed notch in the Fremont Weir could achieve just 

such a purpose. 

Estimates of the proportion of fish passing the Fremont Weir into the Yolo Bypass are only 

meaningful for Release Groups 4 and 5. While the estimate for Release Group 3 is above 0, this release 

was conducted just before the Fremont Weir overtopped, and most tagged fish likely passed the weir 

before it was overtopped (fig. 2). Entrainment into Yolo Bypass differed greatly between the last two 

release groups, however. Over 80 percent of fish were estimated to have migrated through Yolo 

Bypass during Release Group 4 (fig. 5), when flow into Yolo Bypass at the Fremont Weir was at its

peak. This estimate seems to indicate that when enough water goes into the Yolo Bypass, most fish 

will migrate via this route. However, less than 5 percent of fish migrated through the Yolo Bypass 

during Release Group 5. This release was conducted only 2 days later, while Yolo Bypass flow at 

Fremont Weir was declining but still substantial. Analysis of near-field acoustic-tagged fish tracks 

conducted for this study indicate that as discharge over the Fremont Weir increases, mean crosssectional fish position moved closer to the weir (Blake and others, 2017). In contrast, as flows near 

Fremont Weir decrease, but are still great enough to provide substantial flow into the Yolo Bypass, 

mean fish position moves away from the bank formed by the weir and toward the Sacramento River 

centerline. Thus, it seems reasonable to posit that at certain overtopping flow levels, fish are not close 

enough to the Fremont Weir to become entrained over the weir and into the Yolo Bypass, even though 

a substantial fraction of river flow is entering the Bypass. These results suggest that any proposed 

notch in the Fremont Weir should be carefully designed to have the desired effect of diverting both 

water and fish into the Yolo Bypass. Additionally, we remind the reader that these results are from a 

study involving only actively migrating juvenile Chinook salmon smolts, and that salmon in different 
26 

life stages will likely behave differently. For example, the Yolo Bypass has been viewed as potential 

rearing habitat for juvenile salmon. Actively migrating smolts are not likely to see a benefit from 

increased rearing habitat, but salmon fry very well may benefit. We encourage further research on the 

applied potential benefits of access to the Yolo Bypass for various life stages.

Acknowledgments

We would like to thank the USGS California Water Science Center for their efforts in 

coordinating this study, as well as for technical assistance. Additionally, the U.S. Army Corps of 

Engineers and University of California Davis assisted in providing and deploying acoustic 

hydrophones and receivers used for the study. Funding for this study was provided by the California 

Department of Water Resources under interagency agreement 4600009512. 

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29 

Appendix 1. Fundamental Reach-Specific Parameter Estimates

Table 1-1. Directly estimated parameters for reach-specific survival and detection probability, for junction-specific 

entrainment probability, and for reach-specific gamma distributed travel time parameters.

[Lower and Upper credible limit: Denotes the 5th and 95th percentiles of the posterior distributions for each parameter, 

respectively]

Name Release Median

Lower 

credible

limit

Upper 

credible 

limit

Location description

Survival parameters

SA1 1 0.880 0.839 0.912 Tisdale to Verona

2 0.861 0.816 0.905

3 0.939 0.885 0.983

4 0.962 0.876 0.997

5 0.983 0.930 0.999

SA2 1 0.798 0.750 0.841 Fremont Weir to Freeport

2 0.937 0.889 0.971

3 0.982 0.935 0.999

4 0.980 0.929 0.998

5 0.991 0.963 0.999

SA3 1 0.933 0.895 0.966 Freeport to 

2 0.992 0.970 0.999 Sutter/Steamboat Slough

3 0.977 0.921 0.998

4 0.982 0.936 0.998

5 0.988 0.954 0.999

SA4 1 0.939 0.891 0.975 Sutter/Steamboat Slough to 

2 0.962 0.924 0.988 Georgiana Slough

3 0.976 0.928 0.997

4 0.969 0.898 0.998

5 0.981 0.930 0.999

SA5 1 0.904 0.840 0.949 Georgiana Slough to above 

2 0.976 0.932 0.996 Rio Vista

3 0.975 0.905 0.998

4 0.960 0.875 0.996

5 0.976 0.910 0.998

SA6 1 0.886 0.757 0.986 Above Rio Vista to Chipps 

2 0.793 0.644 0.953 Island

3 0.793 0.628 0.965

4 0.863 0.750 0.965

5 0.920 0.822 0.989

SB1 3 0.980 0.946 0.997 Fremont Weir to I-80 

4 0.910 0.862 0.947 Bridge

5 0.933 0.875 0.981

SB3 3 0.851 0.784 0.905 I-80 Bridge to Cache Slough 4 0.878 0.821 0.922

5 0.773 0.692 0.844

SC41A 1 0.797 0.587 0.973 Sutter Slough to Miner 

2 0.967 0.878 0.997 Slough

3 0.658 0.074 0.979

4 0.795 0.328 0.983

5 0.898 0.131 0.994

SC42A 1 0.781 0.513 0.976 Miner Slough to Cache 

2 0.949 0.811 0.996 Slough

3 0.885 0.655 0.991

Survival parameters—Continued

4 0.813 0.450 0.984

5 0.867 0.587 0.988
30 

Name Release Median

Lower 

credible

limit

Upper 

credible 

limit

Location description

SC6A 1 0.578 0.345 0.823 Cache Slough to Chipps 

2 0.650 0.440 0.878 Island

3 0.832 0.682 0.977

4 0.851 0.772 0.950

5 0.922 0.837 0.989

SC41B 1 0.931 0.765 0.993 Upper Steamboat Slough

2 0.956 0.846 0.996

3 0.939 0.758 0.995

4 0.935 0.757 0.995

5 0.893 0.149 0.995

SC42B 1 0.931 0.759 0.994 Lower Steamboat Slough

2 0.970 0.889 0.997

3 0.917 0.717 0.994

4 0.936 0.762 0.994

5 0.950 0.815 0.996

SC6B 1 0.858 0.670 0.980 Steamboat Slough Exit to 

2 0.872 0.700 0.986 Chipps Island

3 0.810 0.587 0.974

4 0.958 0.827 0.997

5 0.865 0.704 0.977

SD5 1 0.556 0.382 0.785 Georgiana Slough to Lower 

2 0.868 0.744 0.965 Mokelumne

3 0.955 0.863 0.994

4 0.923 0.786 0.988

5 0.954 0.866 0.994

SD6 1 0.375 0.181 0.629 Lower Mokelumne to 

2 0.507 0.334 0.703 Chipps Island

3 0.650 0.452 0.861

4 0.840 0.662 0.970

5 0.686 0.528 0.836

Routing parameters

ΨA1 1 1 1 1 Sacramento River at 

2 1 1 1 Fremont Weir

3 0.988 0.965 0.997

4 0.199 0.110 0.313

5 0.960 0.887 0.992

ΨA2 1 0.691 0.590 0.775 Sacramento River at 

2 0.643 0.506 0.762 Sutter/Steamboat Slough

3 0.650 0.270 0.950

4 0.751 0.546 0.887

5 0.712 0.267 0.998

ΨA3 1 0.729 0.654 0.798 Sacramento River at 

2 0.700 0.631 0.764 Georgiana Slough

3 0.625 0.538 0.711

4 0.787 0.705 0.854

5 0.698 0.619 0.770

ΨB1 1 0 0 0 Yolo Bypass Entrance

2 0 0 0

3 0.012 0.003 0.035

4 0.801 0.687 0.890

5 0.040 0.008 0.113

Routing parameters—Continued

ΨC1A 1 0.204 0.155 0.259 Sutter Slough Entrance

2 0.195 0.135 0.265

3 0.015 0.001 0.310
31 

Name Release Median

Lower 

credible

limit

Upper 

credible 

limit

Location description

4 0.041 0.010 0.131

5 0.160 0.001 0.368

ΨC1B 1 0.105 0.070 0.151 Steamboat Slough Entrance 2 0.162 0.103 0.229

3 0.335 0.049 0.420

4 0.208 0.103 0.323

5 0.128 0.001 0.365

ΨD1 1 0.271 0.202 0.346 Georgiana Slough Entrance

2 0.300 0.236 0.369

3 0.375 0.289 0.462

4 0.213 0.146 0.295

5 0.302 0.230 0.381

Detection probability parameters

PA1 1 0.943 0.909 0.968 Sacramento River at Verona 2 0.516 0.457 0.577

3 0.613 0.539 0.683

4 0.649 0.373 0.877

5 0.716 0.588 0.823

PA2 1 0.989 0.969 0.998 Sacramento River at 

2 0.744 0.687 0.794 Freeport

3 0.105 0.066 0.154

4 0.072 0.038 0.120

5 0.157 0.110 0.213

PA3 1 0.993 0.972 0.999 Sacramento River Below 

2 0.962 0.925 0.984 Steamboat Slough

3 0.840 0.768 0.899

4 0.182 0.117 0.266

5 0.245 0.178 0.324

PA4 1 0.990 0.957 0.999 Sacramento River Below 

2 0.707 0.621 0.786 Georgiana Slough

3 0.325 0.225 0.436

4 0.063 0.024 0.130

5 0.102 0.050 0.176

PA5 1 0.988 0.947 0.999 Sacramento River Near Rio 

2 0.989 0.953 0.999 Vista

3 0.982 0.926 0.999

4 0.662 0.535 0.806

5 0.840 0.718 0.944

PA6 1 0.889 0.770 0.987 Sacramento River at Chipps 

2 0.833 0.698 0.978 Island

3 0.831 0.705 0.977

4 0.960 0.871 0.997

5 0.939 0.869 0.993

PB2 3 0.945 0.900 0.976 Yolo Bypass at I-80 Bridge

4 0.976 0.943 0.993

5 0.864 0.791 0.921

PC3A 1 0.928 0.801 0.989 Sutter Slough Near Entrance 2 0.506 0.345 0.711

3 0.207 0.007 0.889

4 0.337 0.061 0.880

5 0.052 0.003 0.848

Detection probability parameters—Continued

PC5A 1 0.930 0.735 0.994 Cache Slough Near Rio 

2 0.878 0.686 0.988 Vista

3 0.988 0.950 0.999
32 

Name Release Median

Lower 

credible

limit

Upper 

credible 

limit

Location description

4 0.992 0.967 0.999

5 0.989 0.953 0.999

PC3B 1 0.938 0.779 0.995 Steamboat Slough Near 

2 0.591 0.394 0.875 Entrance

3 0.067 0.021 0.359

4 0.168 0.062 0.392

5 0.054 0.003 0.811

PC5B 1 0.961 0.849 0.997 Steamboat Slough Near Rio 

2 0.928 0.815 0.993 Vista

3 0.872 0.718 0.969

4 0.669 0.400 0.911

5 0.755 0.541 0.962

PD4 1 0.955 0.827 0.997 Georgiana Slough Near 

2 0.977 0.902 0.998 Entrance

3 0.977 0.905 0.998

4 0.963 0.842 0.997

5 0.976 0.900 0.998

PD5 1 0.883 0.602 0.991 Lower Mokelumne River

2 0.954 0.829 0.997

3 0.969 0.886 0.997

4 0.955 0.828 0.996

5 0.969 0.883 0.997

Travel time parameters

ααA1 1 2.356 2.135 2.589 Sacramento River at Verona 2 4.338 3.904 4.778

3 3.318 2.941 3.727

4 1.420 0.945 1.943

5 2.608 2.153 3.121

ααA2 1 2.995 2.708 3.304 Sacramento River at 

2 2.482 2.181 2.794 Freeport

3 2.130 1.678 2.600

4 1.260 0.921 1.608

5 1.722 1.410 2.060

ααA3 1 1.494 1.332 1.661 Sacramento River Below 

2 1.370 1.217 1.537 Steamboat Slough

3 1.029 0.684 1.418

4 0.495 0.241 0.832

5 0.546 0.291 0.839

ααA4 1 0.928 0.802 1.063 Sutter/Steamboat Slough to 

2 0.822 0.710 0.944 Georgiana Slough

3 0.711 0.563 0.879

4 0.426 0.223 0.683

5 0.520 0.341 0.743

ααA5 1 1.286 1.096 1.496 Georgiana Slough to above 

2 1.240 1.056 1.449 Rio Vista

3 1.025 0.788 1.288

4 0.561 0.300 0.871

5 0.625 0.397 0.883

ααA6 1 4.348 3.827 4.897 Above Rio Vista to Chipps 

2 6.389 5.649 7.144 Island

3 6.458 5.594 7.392

Travel time parameters—Continued

4 2.163 1.772 2.590

5 3.610 3.100 4.149

ααB1 3 1.784 1.550 2.033 Fremont Weir to I-80 
33 

Name Release Median

Lower 

credible

limit

Upper 

credible 

limit

Location description

4 3.236 2.840 3.674 Bridge 5 3.385 2.970 3.831

ααB3

3 7.473 6.713 8.268 I-80 Bridge to Cache Slough 4 3.329 2.923 3.768 5 3.628 3.172 4.117

ααCAA

1 1.520 1.093 2.002 Sutter Slough to Miner 2 1.535 1.083 2.062 Slough 3 2.279 0.637 13.032 4 1.178 0.412 2.520 5 1.094 0.346 6.637

ααCAB

1 1.630 0.983 2.443 Sutter Slough to Steamboat 2 1.327 0.845 1.943 Slough 3 2.470 0.548 14.671 4 1.242 0.287 7.015 5 0.971 0.365 7.064

ααC6A

1 5.564 4.189 7.037 Cache Slough to Chipps 2 8.350 6.808 10.036 Island 3 5.784 5.140 6.482 4 2.749 2.389 3.140 5 3.838 3.364 4.341

ααCBB

1 1.313 0.921 1.762 Upper Steamboat to Lower 2 1.223 0.901 1.601 Steamboat Slough 3 0.993 0.485 1.658 4 0.629 0.291 1.115 5 0.997 0.382 6.642

ααCBA

1 18.450 8.264 28.906 Upper Steamboat to Miner 2 27.090 19.353 34.505 Slough 3 1.683 0.740 3.407 4 5.616 0.738 13.455 5 1.065 0.355 6.919

ααC6B

1 4.178 3.380 5.089 Steamboat Slough Exit to 2 7.713 6.694 8.801 Chipps Island 3 5.869 4.805 7.049 4 2.003 1.477 2.632 5 3.124 2.491 3.824

ααD5

1 1.737 1.256 2.319 Georgiana Slough to Lower 2 1.878 1.512 2.268 Mokelumne 3 2.287 1.856 2.757 4 1.323 0.967 1.731 5 1.872 1.497 2.295

ααD6

1 6.024 4.322 7.953 Lower Mokelumne to 2 18.588 16.171 21.219 Chipps Island 3 13.980 11.995 16.026 4 8.211 6.766 9.772 5 8.237 6.991 9.636

ββ

1 1.640 1.499 1.786 Entire Delta 2 3.351 3.061 3.651 3 3.596 3.277 3.948 4 1.835 1.640 2.036 5 2.392 2.155 2.644

Publishing support provided by the U.S. Geological Survey

Science Publishing Network, Tacoma Publishing Service Center

For more information concerning the research in this report, contact the

Director, Western Fisheries Research Center

U.S. Geological Survey

6505 NE 65th Street

Seattle, Washington 98115 

https://wfrc.usgs.gov/
ISSN 2331-1258 (online)

https://doi.org/10.3133/ofr20181118

Pope and others—Survival, Travel Time, and Utilization of Yolo Bypass, California, by Outmigrating Acoustic-Tagged Late-Fall Chinook Salmon—Open-File Report 2018–1118