U.S. Fish and Wildlife Service

Annual Report:

Juvenile fish monitoring during the 2010 and 2011 field seasons within the San 

Francisco Estuary, California

Jonathan Speegle, Joseph Kirsch, and Jack Ingram

U.S. Fish and Wildlife Service

Stockton Fish and Wildlife Office

Delta Juvenile Fish Monitoring Program

850 South Guild Ave, Suite 105

Lodi, CA 95240

(209) 334-2968

January 2013
ii

EXECUTIVE SUMMARY

The Delta Juvenile Fish Monitoring Program (DJFMP) has monitored juvenile Chinook salmon 

(Oncorhynchus tshawytscha) within the San Francisco Estuary since 1976 using a combination 

of surface trawls and beach seines. Since 2000, 58 beach seine sites and 3 trawl sites have been 

sampled weekly or biweekly within the Estuary and lower Sacramento and San Joaquin rivers. 

Currently, the objectives of the DJFMP are to determine the abundance and distribution trends of 

unmarked juvenile winter-, fall-, spring-, and late fall-run Chinook salmon migrating through the 

Estuary and report the catch of other fishes of management concern including four native species 

(Central Valley steelhead Oncorhynchus mykiss irideus, delta smelt Hypomesus transpacificus, 

longfin smelt Spirinchus thaleichthys, Sacramento splittail Pogonichthys macrolepidotus) and 

two nonnative species (striped bass Morone saxatilis, and threadfin shad Dorosoma petenense). 

This report describes the monitoring and data collected during the 2010 and 2011 field seasons.

While sampling efforts were roughly equal, in-river flows were markedly higher in the 2011 

field season compared to that of the 2010 field season and provided for an interesting contrast in 

the relative abundance and/or distribution of the species collected.

We completed 9,112 surface trawl and 3,790 beach seine samples during the 2010 and 2011 field 

seasons. Trawl samples were distributed relatively evenly among sites and seasons. Conversely, 

considerable spatial and temporal variability existed in the number of samples collected at sites 

within nearly all seine regions during the 2010 and 2011 field seasons.

A total of 441,889 fishes, representing 77 different species, were captured during the 2010 and 

2011 field seasons. During the 2010 and 2011 field seasons, approximately 71% (n=109,279) 

and 41% (n=116,649) of the fishes captured during the 2010 and 2011 field seasons were 

identified as species not native to the San Francisco Estuary, respectively. The higher proportion 

of native fishes observed during the 2011 field season relative to the 2010 field season may have 

resulted, in part, from higher recruitment of two native fish species (i.e., Sacramento splittail and 

Chinook salmon) in response to higher in-river flows and cooler water temperatures within the

San Francisco Estuary and its watershed. 

The spatial distribution and abundances of unmarked juvenile Chinook varied temporally and 

among races. In general, unmarked juvenile winter-run Chinook salmon were detected by the 

DJFMP from October through April. Unmarked juvenile spring-run Chinook salmon were 

detected from October through May. However, unmarked juvenile fall- and late fall-run Chinook 

salmon were generally detected throughout the year. The abundance of unmarked winter- and 

late fall-run smolt sized juvenile Chinook salmon (fork length ≥ 70 mm) reached record lows 

during the 2010 and 2011 field seasons. Whereas the abundance of unmarked fall- and springrun smolt sized juvenile Chinook salmon increased during the 2010 and 2011 field seasons from 

near record lows observed in 2008. Similarly, the relative abundance of fry sized juvenile 

Chinook salmon (fork length < 70 mm) for all races increased during the 2010 and the 2011 field 

seasons from near record lows observed in 2008 and 2009. The higher abundance of most 

unmarked juvenile Chinook salmon during the 2011 field season was likely in response to higher 

adult escapement combined with a higher river discharge.
iii

The DJFMP observed the majority of steelhead from January to May during the 2010 and 2011 

field seasons. Because of consistently low captures, few inter-annual trends could be discerned. 

However, there is evidence that the number of wild steelhead within the Estuary appears to have 

steadily declined since the 1998 field season.

Due to consistently low and/or isolated catches, few inferences could be made regarding the 

relative abundance or distribution of delta smelt or longfin smelt within the Estuary. However, 

we detected some adult delta smelt and longfin smelt in beach seine and trawl samples during 

their upstream migration from the low salinity zone (1-6 ppt) during the winter and spring or 

when the low salinity zone was in proximity to a sample location (i.e., Chipps Island). Overall, 

the DJFMP should be viewed only as a source of anecdotal information regarding these species, 

since neither delta smelt nor longfin smelt were targeted species and in some cases (i.e., Chipps 

Island) sampling efforts were curtailed when delta smelt were present in the sampling area to 

minimize incidental take.

Juvenile Sacramento splittail were generally detected from May through July during the 2010 

and 2011 field seasons. The relative abundance of juvenile Sacramento splittail reached a record 

high during the 2011 field season in all seine regions. The increase in relative abundance during 

the 2011 field season was likely in response to higher river discharges and seasonal floodplain 

inundation, particularly within the San Joaquin River basin.

In general, the relative abundances of threadfin shad responded negatively to higher river 

discharges and cooler water temperatures within and among field seasons. Most threadfin shad 

were observed during the summer and fall months during the 2010 and 2011 field seasons. Low 

densities of threadfin shad were observed from February to June; likely in response to poor 

survival caused by cool water temperatures during the month of January. The relative abundance 

of threadfin shad in most sampling locations reached near record lows during the 2011 field 

season. 

The DJFMP captured juvenile or sub-adult striped bass primarily from July to October during the 

2010 and 2011 field seasons. The relative abundance of striped bass reached near record lows 

during the 2011 field season at all trawl sites. However, no discernible inter-annual trend in 

striped bass relative abundance could be detected within and among seine regions since the 2000 

field season. 

The correct citation for this report is:

Speegle, J., J. Kirsch, and J. Ingram. 2013. Annual report: juvenile fish monitoring during the 

2010 and 2011 field seasons within the San Francisco Estuary, California. Stockton Fish and 

Wildlife Office, United States Fish and Wildlife Service, Lodi, California.
iv

TABLE OF CONTENTS

 Page 

EXECUTIVE SUMMARY ............................................................................................... ii

ACKNOWLEDGMENTS ...................................................................................................v

TABLE OF ACRONYMS................................................................................................. vi

INTRODUCTION ...............................................................................................................1

Background..............................................................................................................1

Current Objectives...................................................................................................2

METHODS ..........................................................................................................................3

Monitoring Locations...............................................................................................3

Beach Seine Methodology........................................................................................5

Trawl Methodology..................................................................................................7

Fish Processing......................................................................................................10

Relative Abundance Calculations..........................................................................12

Length Frequency ..................................................................................................14

Absolute Abundance Calculations.........................................................................14

River Flow Conditions...........................................................................................15

RESULTS AND DISCUSSION........................................................................................16

Chinook Salmon.....................................................................................................18

Steelhead................................................................................................................55

Delta Smelt.............................................................................................................68

Longfin Smelt .........................................................................................................75

Sacramento Splittail...............................................................................................80

Threadfin Shad.......................................................................................................92

Striped Bass .........................................................................................................104

REFERENCES ................................................................................................................116

APPENDIX......................................................................................................................122
v

ACKNOWLEDGMENTS

All fish sampling presented in this report was conducted for and funded by the Interagency 

Ecological Program (IEP) for the San Francisco Estuary. Members of the IEP include three state 

agencies (California Department of Water Resources (CDWR), California Department of Fish 

and Wildlife (CDFW), and State Water Resources Control Board) and six federal agencies (U.S. 

Bureau of Reclamation, U.S. Geological Survey (USGS), U.S. Fish and Wildlife Service

(USFWS), National Marine Fisheries Service (NMFS), U.S. Army Corps of Engineers, and the 

U.S. Environmental Protection Agency).

We also acknowledge and extend gratitude to the many biological science field technicians and 

boat operators who spent countless hours under all environmental conditions to collect these 

data. We would like to especially thank Amber Aguilera, Denise Barnard, Ken Behen, Crystal 

Castle, Amy Combs, Dustin Dinh, David Dominguez, Kate Erly, Kyle Fronte, Carlie Jackson, 

David LaPlante, Jerrica Lewis, Mike Marshall, Paul Miklos, Greg Nelson, Scott Porter, Pam 

Tarelli, Phil Voong, Jolene Willis, and Julie Wolford for assistance with sampling, Jackie Hagen, 

Ron Hagins, Patrick Hapgood, and Bill Powell for boating assistance, John Pedretti for his help 

with fish identification, and Angie Bourandas for helping oversee data entry and quality control 

during the 2010 and 2011 field seasons.

Disclaimer: The mention of trade names or commercial products in this report does not constitute 

endorsement or recommendation for use by the Federal government.
vi

TABLE OF ACRONYMS

The following acronyms have been used in this report:

CESA – California Endangered Species Act

CDFW – California Department of Fish & Wildlife

CDWR – California Department of Water Resources

CNFH – Coleman National Fish Hatchery

CPUE – Catch Per Unit Effort

CVP – Central Valley Project

CWT – Coded Wire Tag

DJFMP – Delta Juvenile Fish Monitoring Program

ESA – Federal Endangered Species Act

FL – Fork Length

FRFH – Feather River Fish Hatchery

KDTR – Kodiak Trawl

MWTR – Mid-water Trawl

NMFS – National Marine Fisheries Service

RM – River Mile

RMIS – Regional Mark Information System

SD – Standard Deviation

SE – Standard Error

SJRGA – San Joaquin River Group Authority

STFWO – Stockton Fish & Wildlife Office

SWP – State Water Project

USFWS – United States Fish & Wildlife Service

USGS – United States Geological Survey
1

INTRODUCTION

The San Francisco Estuary is notably the largest estuary in California and provides spawning 

habitat, nursery habitat, and migratory pathways for over 40 freshwater, estuarine, euryhaline 

marine, and anadromous fish species (Moyle 2002). Historically, the Estuary was maintained by 

natural runoff from an estimated 40% of California's surface area (Nichols et al. 1986). However, 

perpetual increases in agriculture and urbanization throughout California over the last century, 

coupled with California's Mediterranean climate (i.e., wet winters and dry summers), have

necessitated intense water management within the Sacramento – San Joaquin River Basin, 

resulting in the damming of most rivers, confinement of channels, and water diversions and

exports (Nichols et al. 1986). Anthropogenic activities have subjected the San Francisco Estuary

to artificial flow regimes that can have profound impacts on aquatic habitats and organisms 

(Stevens and Miller 1983; Brandes and McLain 2001; Bunn and Arthington 2002; Kimmerer 

2002; Feyrer and Healey 2003). As a result, fish species of management concern within the 

Estuary have been studied and monitored by the Delta Juvenile Fish Monitoring Program 

(DJFMP) of the Stockton Fish and Wildlife Office to assess and minimize the effects of water 

operations on fish populations.

Background

The DJFMP, working in conjunction with IEP members, has monitored the relative abundance 

and distribution of juvenile fishes annually within the San Francisco Estuary since 1976 

(Brandes et al. 2000). The specific goals of the DJFMP have evolved since inception based on 

both water management actions and listings under the Endangered Species acts. Prior to 1982, 

goals of the DJFMP were to (1) monitor the relative abundance of juvenile Chinook salmon to 

determine the importance of the San Francisco Estuary as a nursery habitat and (2) determine 

how reduced river flows below the proposed Peripheral Canal intake would affect the survival of 

juvenile Chinook salmon in the San Francisco Estuary (Brandes et al. 2000). After the defeat of 

the Peripheral Canal proposal in 1982, the goals of the DJFMP were changed to evaluating the 

impact of through-Delta water conveyance on juvenile Chinook salmon distribution and survival

(Brandes et al. 2000).

Prior to 1992, the majority of the annual juvenile Chinook salmon monitoring was conducted 

between April and June during peak Chinook salmon emigration within the San Francisco 

Estuary. However, after the Sacramento River winter-run Chinook salmon was listed as 

“Endangered” under the California Endangered Species Act (CESA) in 1989 (CDFG 2005) and 

under the Endangered Species Act of 1973 (ESA) in 1994 (NMFS 2009), goals expanded to 

include monitoring the abundance, distribution, and survival of juvenile Chinook salmon in the 

Estuary annually from September to June (Brandes et al. 2000). Other listings of fishes occurring 

in the San Francisco Estuary followed (USFWS 1995; CDFG 2005; NMFS 2009). For example, 

the delta smelt was listed as “Threatened” under the CESA and ESA in 1993, the Central Valley 

steelhead and spring-run Chinook salmon were listed as “Threatened” under both the CESA and 

ESA in 1999, and the longfin smelt was listed as “Threatened” under the CESA in 2009

(USFWS 1995; CDFG 2005; CDFG 2009; NMFS 2009).
2

In response to the additional fish listings and a program review in 2000, the DJFMP expanded its 

goals further to include monitoring all juvenile fishes throughout the year to detect trends in the 

relative abundance and distribution of fish species of management concern in the San Francisco 

Estuary. Although the DJFMP had historically recorded data on non-salmonid fishes, it was not 

until 2001 that program objectives were broadened to reflect the value of gathering information 

on non-salmonid species. In recognition of the value of understanding assemblage-level 

responses and biotic interactions in the Delta, data from all species captured have been reported 

in the DJFMP annual reports since 2006.

Current Objectives

The fish data collected by the DJFMP are intended to provide basic biological and demographic

information that can be used by natural resource managers to evaluate the effectiveness of water 

operations and fish management practices within the San Francisco Estuary and its watershed.

This report will primarily focus on non-benthic fishes of management concern based on the 

limitations of the sampling methodologies and locations used by the DJFMP. Fishes of 

management concern include juvenile fall-, late fall-, winter-, and spring-run Chinook salmon, 

steelhead, delta smelt, longfin smelt, Sacramento splittail, striped bass, and threadfin shad; 

USFWS 1995; CDFG 2009; NMFS 2009; MacNally et al. 2010; USFWS 2011). The objectives 

of the annual report for the 2010 (August 1, 2009 to July 31, 2010) and 2011 (August 1, 2010 to 

July 31, 2011) field seasons were to:

1. Determine the relative abundance, and spatial and temporal distributions of unmarked 

juvenile fall-, late fall-, winter-, and spring-run Chinook salmon migrating through the 

San Francisco Estuary.

2. Report the recovery of marked juvenile fall-, late-fall, winter-, and spring-run Chinook 

salmon migrating through the San Francisco Estuary.

3. Estimate the annual absolute abundance of unmarked juvenile fall-, late fall-, winter-, and 

spring-run Chinook salmon emigrating out of the Delta.

4. Report the relative abundance of unmarked juvenile Chinook salmon near Sacramento to 

inform future water operations during periods of possible water diversion.

5. Report the relative abundance, and spatial and temporal distributions of other fishes of 

management concern observed within the San Francisco Estuary.

6. Relate the relative abundance of fish species of management concern to river discharge.

7. Determine the length frequency distributions of fish species of management concern

captured during the 2010 and 2011 field seasons. 
3

METHODS

Monitoring Locations

The San Francisco Estuary consists of three distinct segments: the Sacramento – San Joaquin 

Delta, Suisun Bay, and San Francisco Bay (Moyle 2002). During the 2010 and 2011 field 

seasons, the DJFMP sampled at 58 beach seine sites and 3 trawl sites located within the lower 

Sacramento and San Joaquin rivers, at and between the entry and exit points of the Delta, and 

within the San Francisco Bay (Figure 1; Table A1). The DJFMP has sampled the majority of 

these sites annually since the mid-1990s (Table A1). 

We used surface trawls to facilitate our understanding of the relative abundance of fishes 

migrating through the San Francisco Estuary. Trawl sites were located at the entry (Sacramento 

and Mossdale Trawl sites) and exit (Chipps Island Trawl Site) points of the Sacramento – San 

Joaquin Delta (Figure 1; Table A1). The DJFMP attempted to sample each trawl site three days 

per week, ten times per day throughout the 2010 and 2011 field seasons. Trawl sites were 

generally sampled Monday, Wednesday, and Friday each week throughout the field season to 

maximize temporal coverage. The CDFG has traditionally sampled the Mossdale Trawl Site, 

following similar methodologies, in place of the DJFMP between April and June (SJRGA 2005). 

Data collected from both the DJFMP and CDFG at the Mossdale Trawl Site are included in this 

report.

We used beach seines to quantify the spatial distribution of fishes occurring in shallow habitats 

(e.g., beaches and boat ramps <1.2 m in depth) throughout the lower Sacramento and San 

Joaquin rivers and the San Francisco Estuary. Beach seine sites were stratified into seven 

geographic regions: (1) Lower Sacramento River Seine, (2) North Delta Seine, (3) Central Delta 

Seine, (4) South Delta Seine, (5) Lower San Joaquin River Seine (6) San Francisco and San 

Pablo Bay Seine and (7) Sacramento Area Seine (Figure 1; Table A1). Seine regions were 

delineated by proximity to canals or water bypasses where fish may be diverted from historical 

migration routes. Fish movement patterns within regions were assumed to be similar.

In this dynamic system, occasional changes in river flow or environmental conditions prevent 

sampling or make it necessary to temporarily relocate seine sites. If new seine sites were needed, 

we attempted to relocate the site to another suitable location with similar habitat (e.g., 

hydrogeomorphic characteristics) that was less than 100m from the original site. Different 

combinations of beach seine sites were sampled within the Lower San Joaquin River Region 

during the 2010 and 2011 field seasons based on fluctuations in site accessibility as a result of

river flow conditions (Table A1). When the discharge of the lower San Joaquin River was greater 

than 51 m

3

/s, the historic beach seine sites were accessible by boat and sampled. Conversely, 

when the discharge of the lower San Joaquin River was below 51m3/s, the river was no longer 

navigable by boat and only the beach seine sites that were accessible by land were sampled 

(Table A1). More information on seine site relocations or other seine monitoring site 

modifications can be found in the STFWO Metadata file at

http://www.fws.gov/stockton/jfmp/datamanagement.asp.
4

We attempted to sample fishes at the beach seine sites one day per week, one time per day 

throughout the 2010 and 2011 field seasons within all seine regions except the Sacramento Area 

Seine Region, the Lower San Joaquin River Region, and the San Francisco and San Pablo Bay 

Seine Region. The beach seine sites that were located within the Sacramento Area Seine Region 

were generally sampled three days per week, one time per day from October 1st to January 31 st

to better detect ESA listed winter- and spring-run Chinook salmon migrating near the Delta 

Cross Channel during periods of potential water diversion (Brandes et al. 2000). The beach seine 

sites that were located within the Lower San Joaquin River Region were generally sampled one 

day per week, one time per day from January 1st to July 31st and one day every two weeks from 

August 1st to December 31st based on minimal occurrence of fishes of management concern 

coupled with poor accessibility to seine sites. The beach seine sites that were located within the 

San Francisco and San Pablo Bay Seine Region were generally sampled one day per two weeks, 

one time per day throughout the 2010 and 2011 field seasons based on logistical limitations and 

the low occurrence of fish species of management concern.

Figure 1. Sites sampled during the 2010 and 2011 field seasons within the lower 

Sacramento and San Joaquin rivers and San Francisco Estuary. 
5

Beach Seine Methodology

Sampling at beach seine sites was conducted between sunrise and sunset. We sampled using a

15.2 x 1.3 m beach seine net with 3 mm delta square mesh, a 1.2 m bag in the center of the net, 

and a float line and lead line attached to 1.8 m tall wooden poles on each side. In general, beach 

seines were deployed along the shoreline by two crew members within unobstructed habitats 

including boat ramps, mud banks, and sandy beaches. When sampling mud dominated habitats 

(i.e., dominated by substrata with particles < 62.5 μm in diameter), we applied rollers to the lead 

line of the beach seine to limit the net from sinking into the substrate and impeding the 

completion of the seine.

The beach seines were generally deployed starting from the downstream portion of each site to 

limit disturbance (e.g., displacement of sediment into the site). Crew member 1 distributed the 

seine into the water, perpendicular from the shoreline, as crew member 2 secured the opposite 

end of the seine to the shoreline (Figure 2a). After reaching a depth of up to 1.2 m, a distance 

(i.e., length) of up to15 m, or an obstacle, crew member 1 measured and recorded the distance to 

the shoreline and depth to the nearest 1 m and 0.1 m, respectively (Figure 3). Obstacles were 

defined as structure that could compromise safety or gear efficiency including steep banks or 

holes, fast water current, submerged aquatic vegetation, or large woody debris. Next, crew 

member 2 carried their end of the seine to crew member 1 and placed their end of the seine in the 

same location as crew member 1. The seine was then distributed from that point upstream and as 

parallel to the shoreline as possible by crew member 1 (Figure 2b). When crew member 1 

reached a depth of up to 1.2 m, a distance (i.e., width) of up to15 m, or an obstacle that could 

compromise safety or gear efficiency, crew member 1 would stop and the width and depth of the 

seine was measured to the nearest 1 m and 0.1 m, respectively (Figure 3). If the depths of the 

seine varied between measurements, the maximum seine depth was obtained by averaging the 

two depth measurements. Lastly, crew members 1 and 2 pulled the ends of the seine

simultaneously toward (i.e., perpendicular) the shoreline while attempting to maintain the 

starting distance (i.e., seine width) apart (Figure 2c). The net was continuously pulled towards 

the shoreline until the lead line of the seine’s bag was on shore (Figure 2d). After the seine haul 

was completed, all fish were collected from the bag and other parts of the seine and placed in a 

holding container filled with river water for processing. 
6

Figure 2. Photographs of the DJFMP conducting a beach seine at station 

SR024E on the bank of the Sacramento River: seine (a) deployed 

downstream of site, (b) distributed upstream parallel to the shoreline, 

(c) pulled in toward the shoreline, and (d) position at the end of a haul.

Figure 3. Schematic diagram of beach seine measurements: (a) three-dimensional view and (b) 

overhead view.

Length

(a)

Length

Width

Shore

Depth 1 Depth 2

(b)

Width

Shore

Depth 1

Depth 2

Length

(a)

(a)

(b) (d)

(c)
7

Trawl Methodology

We sampled at trawl sites with Kodiak (KDTR) and mid-water (MWTR) trawls. The DJFMP 

exclusively uses a MWTR at the Chipps Island Trawl Site and a KDTR at the Mossdale Trawl 

Site. The Sacramento Trawl Site has exclusively used a MWTR prior to 1994, and has used a 

KDTR from October to March and a MWTR for the remainder of each field season thereafter

(Brandes et al. 2000). The KDTR has been used in place of the MWTR at the Sacramento Trawl 

Site to maximize the capture of larger Chinook salmon (Brandes et al. 2000).

During each sampling day, we attempted a maximum of ten 20-minute tows between sunrise and 

sunset, at all trawl sites. All tows were conducted facing upstream in the middle of the channel at

the Sacramento and Mossdale Trawl sites, which constitute a reach length approximately 6.5 km 

and 3 km, respectively. In contrast, tows were generally conducted facing both upstream and 

downstream, regardless of tidal stage, in the north, south, and middle portions of the channel at 

the Chipps Island Trawl Site, which constitutes a reach length of approximately 4 km. The 

MWTR and KDTR nets were towed by one and two boats, respectively, in the top few meters of 

the water column at a speed necessary and distance apart (for KDTR) to ensure the net mouth 

remained fully extended and submerged. The measure of the distance traveled during each tow 

was recorded using a mechanical flow meter (General Oceanics, Model #2030). In general, the 

Sacramento MWTR net was towed at speeds between 0.7-1.0 meters per second (m/s), the 

Chipps Island MWTR net was towed at speeds between 0.9-1.12 m/s, and the KDTR nets were

towed at speeds between 0.45-0.67 m/s at both the Mossdale and Sacramento Trawl sites.

 

The Sacramento MWTR net was composed of six panels, each decreasing in mesh size towards 

the cod end (Figure 4). The mesh size for each panel ranged from 20.3 cm stretch at the mouth 

to 0.6 cm stretch just before the cod end. The cod end was composed of 0.3 cm weave mesh. 

The fully extended mouth size was 4.15 x 5 m. Two depressors and hydrofoils enabled the net to 

remain at the top few meters of the water column while sampling. Depressors were made of 0.7 

cm thick stainless steel (one on each side of the net lead line) and were attached to the net with 

shackles to extend the bottom line of the mouth. Hydrofoils were made of 0.7 cm thick

aluminum plates with split floats (one on each side of the net float line) and were attached to the 

net with shackles to extend the top of the net at the water’s surface. On each side of the net, the 

depressor and hydrofoil were connected to the boat using a 30.5 m Amsteel rope bridle (0.64 cm 

diameter). The net was fished approximately 30 m behind the boat. 

The MWTR net used at the Chipps Island Trawl Site was similar in construction to the MWTR 

net used at the Sacramento Trawl Site (Figure 5). There were five panels, each with decreasing 

mesh size towards the cod end. The mesh size for each panel ranged from 10.2 cm stretch at the 

mouth to 2.5 cm stretch just before the cod end. The cod end was composed of 0.8 cm knotless 

material. The fully extended mouth size of the Chipps Island MWTR net was 7.64 x 9.65 m. The 

depressors and hydrofoils of the Chipps Island MWTR were larger and were connected to the 

boat identically to those on the Sacramento MWTR. On each side of the net, the depressor and 

hydrofoil were connected to the boat using a 30.5 m Amsteel rope bridle (0.6 cm diameter)

attached to a 15.2 m tow rope (0.95 cm diameter). As a result, the Chipps Island MWTR net was 

fished approximately 45 m behind the boat.
8

Figure 4. Schematic drawing of mid-water trawl net (top), and hydrofoils and depressors 

(bottom) used at the Sacramento Trawl Site during the 2010 and 2011 field seasons.

Depressor

20.3 cm stretch 

mesh

10.2 cm 

stretch mesh

7.6 cm stretch 

mesh

5.1 cm 

stretch mesh

2.5 cm stretch 

mesh

1 cm stretch 

mesh

0.3 cm weave 

mesh cod end

Mouth Opening

4.15 x 5 m 

Hydrofoil

Hydrofoil

Depressor

15.2 cm

30.5 cm

53.3 cm

split 20.3 x15.2 cm 

seine float secured 

with 

stainless bolts

15.2 cm

Hydrofoil -Top View Hydrofoil -Side View

seine float

Depressor -Top View Depressor -Side View

30.5 cm

45.7 cm

19.1 cm

5.1 cm

curved

steel

foot

1.3 cm holes

float

19.1 cm

30.5m bridle 

ropes
9

Figure 5. Schematic drawing of mid-water trawl net (top) and hydrofoils and depressors (bottom) 

used at the Chipps Island Trawl Site during the 2010 and 2011 field seasons.

22.9 cm

10.2 cm 

stretch mesh

7.6 cm stretch 

mesh

5.1 cm 

stretch mesh

2.5 cm stretch 

mesh

0.8 cm weave 

mesh cod 

end

3.8 cm 

stretch mesh

Mouth Opening

7.64 x 9.65 m

Depressor

Hydrofoil

Hydrofoil

Depressor

40.6 cm

61.0 cm

split 38.1 x 15.2 cm 

seine float secured 

with stainless bolts

22.9 cm

Hydrofoil -Top View Hydrofoil -Side View

seine float

Depressor -Top View Depressor -Side View

45.7 cm

61.0 cm

22.9 cm

6.4 cm

curved

steel

foot

1.3 cm holes

float

22.9 cm

30.5m bridle 

ropes
10

The KDTR nets used at the Mossdale and Sacramento Trawl sites were composed of five panels, 

each decreasing in mesh size towards a live box at the cod end (Figure 6). The mesh size for each 

panel ranged from 5.1 cm stretch at the mouth to 0.6 cm stretch just before the live box. The live 

box (36 cm wide x 36 cm tall x 49 cm long) was composed of 0.18 cm think aluminum that was 

perforated with numerous 0.46 cm diameter holes. The live box contained several internal baffles 

to minimize fish mortality and stress due to flow pressure. The fully extended mouth size of the 

KDTR nets were 1.96 x 7.62 m. A float line and lead line enabled the nets to remain at the top 

few meters of the water column while sampling. In addition, at the front of each wing of the net 

was a 1.83 m bar with floats at the top and weights at the bottom to keep depth constant while 

sampling. The KDTR nets were connected to the boats using a 2.3 m rope bridle (2.4 cm 

diameter) attached to a 30.5 m tow rope (0.95 cm diameter) on each side of the net. The net was 

fished approximately 31 m from the boats. 

Figure 6. Schematic drawing of Kodiak trawl net used at Sacramento and Mossdale Trawl sites

during the 2010 and 2011 field seasons.

At the end of each tow, the MWTR nets were retrieved by the towing vessel using winches to 

collect all the fishes observed in the cod ends. Whereas at the end of each tow using the KDTR 

nets, the two towing vessels (i.e., net and chase boats) would come together and the chase boat 

would transfer its tow rope to the net boat. The crew on the chase boat would then retrieve the 

live box from the KDTR net and collect all the fishes observed. All fishes collected from the cod 

ends or live boxes were placed in a holding container filled with river water for processing.

Fish Processing

We identified all fish in each sample to species or race that were ≥25 mm fork length (FL) , with 

the exception of five species that were readily identified at ≥ 20 mm FL (e.g. Sacramento 

splittail). Prior to release at the site of capture, we measured fish to the nearest 1 mm FL. If 

greater than 50 individuals of a Chinook salmon race or other species of management concern

were collected, a sub sample of at least 50 individuals were randomly measured for FL. Fish that 

5.1 cm

stretch mesh

3.8 cm 

stretch mesh

2.5 cm

stretch mesh 1.3 cm

stretch mesh

0.6 cm

stretch mesh

live box 

Mouth opening

1.96 x 7.62 m

1.83 m bar

Float line

Lead line

float 

2.3m bridle 

ropes

30.5m tow 

rope
11

could not be accurately identified in the field were initially preserved in the field and brought 

back to the laboratory. Preserved fishes were later identified to species or race and measured for 

FL.

Only juvenile Chinook salmon and steelhead with missing (i.e., clipped) adipose fins were 

considered marked fish. Fish possessing other forms of marks (e.g., stain dye, disc tags, hydroacoustic tags, etc.) were not included within this report to further minimize the influence of

recaptures and/or unnatural occupancy induced by other fishery investigations. All marked 

juvenile steelhead were considered to be reared in a hatchery and all unmarked juvenile steelhead 

were considered wild (i.e., spawned outside of a hatchery). Hatcheries within the Central Valley 

have marked nearly all hatchery reared steelhead for management purposes since 1997 (Kevin 

Niemela, USFWS, personal communication). All marked juvenile Chinook salmon during the 

2010 and 2011 field seasons were considered hatchery reared and assumed to contain a coded 

wire tag (CWT). In general, hatcheries have attempted to mark and tag most winter-, spring- and 

late fall-run juvenile Chinook salmon within the Central Valley. Conversely, hatchery marking 

ad tagging rates of juvenile fall-run Chinook salmon have varied considerably (5-95%; Johnson 

2004). Starting in 2007, Central Valley hatcheries began implementing the constant fractional 

marking of produced juvenile fall-run Chinook salmon where at least 25% of individuals are 

marked and tagged (Kevin Niemela, USFWS, personal communication). Therefore, we 

considered all unmarked juvenile Chinook salmon either wild (i.e., spawned outside of a 

hatchery) or unmarked hatchery reared individuals. 

Because recovered CWTs can provide a variety of important biological information (e.g., an 

individual's race, hatchery of origin, date and location released in the Sacramento-San Joaquin 

River basin, etc.) to natural resource managers, all marked Chinook salmon were preserved in 

the field and brought back to the laboratory. In the laboratory, marked fish were checked for a 

CWT, and, if present, had their CWT removed, read, and recorded. The DJFMP also processed 

the marked Chinook salmon recovered at the State Water Project (SWP) and the Central Valley 

Water Project (CVP) pumping facilities for CWTs during the 2010 field season. CWT data 

collected from the DJFMP, SWP, and CVP were included in this report. We obtained all CWT 

information (e.g., race and release location) from the Regional Mark Information System 

maintained by the Pacific States Marine Fisheries Commission (PSMFC 2012). 

The race of all unmarked juvenile Chinook salmon was determined using the size at date of 

capture river criteria developed by Fisher (1992) and modified by Greene (1992). The 

assumptions associated with the size at date of capture river criteria for the Sacramento-San 

Joaquin River basin include that the (1) spawning of fall-run Chinook salmon occurs between 

1Oct – 31Dec, (2) spawning of late fall-run Chinook salmon occurs between 1Jan – 15Apr, (3) 

spawning of winter-run Chinook salmon occurs between 16Apr – 15Aug, (4) spawning of 

spring-run Chinook salmon occurs between 16Aug – 30Sep, and (5) growth rate of juveniles is 

identical among all races of Chinook salmon (Fisher 1992). Although one or more of these 

assumptions are likely violated (Fisher 1994; Yoshiyama et al. 1998), the river criteria is

currently widely used by managers, and is the only cost effective and logistically feasible way to 

differentiate between the different races of juvenile Chinook salmon in the field. Fisher (1994) 

noted that Chinook salmon races within the Central Valley do appear to spawn at distinctly 

separate time periods except for fall- and spring-run due to the loss of headwater habitats (e.g., 
12

dams), forced coexistence, and subsequent hybridization within the Sacramento River Basin 

(Cope and Slater 1957; Slater 1963). As a result, many of the Chinook salmon characterized as 

spring-run by the size at date of capture river criteria may be fall-run within the Estuary. 

Therefore, the race designations used in this report should be considered a rough approximation 

and not interpreted as definitive, particularly differentiating between fall- and spring-run.

Ongoing genetic analyses of DNA genotypes are underway to help elucidate the accuracy of the 

size at date of capture river criteria to determine all Chinook salmon races within the San 

Francisco Estuary (e.g., Banks et al. 2000; Greig et al. 2003). 

Because fall-run Chinook salmon are reportedly the only race to still occur within the San 

Joaquin River and its main tributaries (Yoshiyama et al. 1998), all juvenile Chinook salmon 

collected at the Mossdale Trawl Site and within the Lower San Joaquin River Seine Region 

(Region 5) were classified as fall-run regardless of their size at the date of capture. Although the 

South and Central Delta Seine regions are located within the San Joaquin River basin, there is 

potential for spring-, winter-, and late fall-run juveniles of Sacramento River origin to migrate 

into the interior delta through the Georgiana Slough, the Delta Cross Channel, and the San 

Joaquin River during water diversions or transfers. Therefore the size at date of capture river 

criteria was still used to determine the race of juvenile Chinook salmon within the South and 

Central Delta Seine regions. 

Relative Abundance Calculations

For each species or race, samples from each gear type were standardized to catch-per-unit effort 

(CPUE) as fish per unit volume (fish / 10,000 m3) using the following equations:

10,000

Depth Width Length

Catch Seine CPUE

2

1

 (1)

10,000

Distance Traveled Net Mouth Area

Catch Trawl CPUE

(2)

Effort was measured by the volume of water sampled by a beach seine, KDTR, or MWTR. By 

assuming a constant slope from the shore to the maximum seine depth, the volume of the water 

sampled using beach seines was calculated by using 1⁄2 x depth in calculations. Because the 

MWTR and KDTR nets do not open completely while under tow and net mouth dimensions vary 

within and among tows (USFWS 1993), we used previously quantified estimates of mean net 

mouth area for this report. The mean net mouth area for MWTR nets used for the Chipps Island 

and Sacramento Trawl sites were obtained from 3-4 physical measurements taken while 

sampling and were reported as 18.58 m2and 5.08 m2, respectively (USFWS 1993). The mean net 

mouth area for KDTR nets used for the Mossdale and Sacramento Trawl sites were obtained by 

extrapolating from the mean net mouth area of the MWTRs and were reported as 12.54 m2

(USFWS 1998). 

The relative abundance of fishes of management concern is presented as mean monthly and 

yearly CPUE values. We treated species, seine regions, trawl sites, and gear types separately for
13

all mean CPUE calculations. Because the number of samples collected varied within and among 

weeks for sites within seine regions and trawl sites, data were summarized using daily, weekly,

monthly, and yearly CPUE averages to minimize the overweighting of sample days and/or

locations.

The mean daily CPUE was calculated as the sum of the trawl or seine CPUE for a trawl or seine 

site during each sample day divided by the number of samples taken each day. The mean weekly 

CPUE was calculated for trawl sites and seine regions as the sum of the mean daily CPUE for a 

trawl or seine site during each sample week divided by the number of days sampled each sample 

week. Subsequently, the mean weekly CPUE values were averaged among seine sites within 

regions. A sample week was defined as Sunday to Saturday. The mean monthly CPUE was 

calculated as the sum of the mean weekly CPUE for a trawl site or seine region during each 

calendar month divided by the number of sample weeks sampled each calendar month. If a 

sample week occurred in more than one calendar month, the sample week was assigned to the 

calendar month that contained the start of the sample week. The mean yearly CPUE was 

calculated as the sum of the mean monthly CPUE for a trawl site or seine region during each 

field season divided by the number of months sampled each field season. 

For inter-annual comparisons of CPUE for all fishes of management concern, we generally 

calculated mean yearly CPUE values starting in the 2000 field season. Sampling methods have 

generally remained consistent from 2000 to the present, including year round sampling and 

standardized gears and mesh sizes. However, we calculated mean yearly CPUE values for the 

Mossdale Trawl Site only during the 2004 through 2011 field seasons for fishes of management 

concern because the start of year round collaborative sampling with the CDFG did not occur 

until January 2003. Prior to the 2004 field season, the only months consistently sampled at the 

Mossdale Trawl Site were April through June by the CDFG. As a result, we did not report only 

April through June data because the DJFMP was not involved in the sampling and these data 

have been already reported annually by the CDFG. In addition, we calculated mean yearly CPUE 

values from April to June during the 1978 through 2011 field seasons for fall-run Chinook 

salmon at Chipps Island. We also calculated mean yearly CPUE values during the 1995 through 

2011 field seasons for all races of juvenile Chinook salmon and steelhead at the Chipps Island

Trawl Site given the site’s historical context for monitoring juvenile salmonids. Prior to the 1995 

field season, the Chipps Island Trawl Site was only consistently sampled by the DJFMP from 

April through June to target juvenile fall-run Chinook salmon, and was sampled in all months 

thereafter to monitor all Chinook salmon races.

We also calculated and graphed the mean monthly CPUE of all fishes of management concern to 

make intra-annual comparisons during the 2010 and 2011 field seasons. We only calculated the 

CPUE of unmarked juvenile winter- and spring-run Chinook salmon for the Sacramento Area 

Seine Region to reflect the objective of monitoring the presence of ESA listed Chinook salmon 

races near the Delta Cross Channel during periods of potential water diversion. The Sacramento 

Area Seine Region was presented separate from all other seine regions based on seasonal 

sampling and the inclusion of data collected at seine sites from other seine regions in the CPUE 

calculations. 
14

Length Frequency 

We calculated length frequency distributions for all species of management concern during the 

2010 and 2011 field seasons for each seine region and trawl site. In cases where fish of 

management concern were “plus counted” or not measured within a sample, the FLs of the 

unmeasured fish were obtained by extrapolating from the fish that were measured within the 

sample. For example, if 100 individuals were plus counted within a sample and 20% of the 

measured individuals had a FL of 45 mm, we assumed that 20 of the 100 plus counted 

individuals also possessed a FL of 45 mm. Because we identified the race of unmarked juvenile 

Chinook salmon using the size at date of capture river criteria, we reported the length frequency 

distribution of all unmarked juvenile Chinook salmon together for each seine region and trawl 

site without any race distinction to avoid bias. 

Absolute Abundance Calculation

The absolute abundance of unmarked juvenile fall-, late fall-, winter-, and spring-run Chinook 

salmon emigrating out of the San Francisco Estuary were estimated monthly from the 1978 to 

2011 field seasons using the data collected at the Chipps Island Trawl Site. Annual comparisons 

of the absolute abundance of unmarked juvenile Chinook salmon were limited to years and

months when sampling was relatively consistent. The monthly absolute abundance of unmarked 

juvenile fall-, late fall-, winter-, or spring-run Chinook salmon (N) was estimated using the 

methods modified from Kjelson (1987) as:

 t x TRR

n

N

i

i

i

(3)

where i indexes months, ni represents the total number of unmarked juveniles collected at the 

Chipps Island Trawl Site during a month, ti represents the fraction of time the Chipps Island 

Trawl Site was sampled during a month, and

TRR

represents the mean trawl recovery rate at the 

Chipps Island Trawl Site. The assumption of this approach is that juvenile salmon are equally 

distributed in time as they migrate past Chipps Island and are never recaptured. 

The trawl recovery rate (TRR) at the Chipps Island Trawl Site was estimated using the capture of 

CWT juvenile Chinook salmon released approximately10 and 12 km upstream of the Chipps 

Island Trawl Site at Sherman Island or Jersey Point, respectively, as:

available

recovered

k

n

n

TRR

(4)

where k indexes release groups at Sherman Island or Jersey Point, nrecovered represents the total 

number of juvenile CWT Chinook salmon within a release group collected at the Chipps Island 

Trawl Site, and navailable represents the number of juvenile CWT Chinook salmon within a release 

group available for collection at the Chipps Island Trawl Site. Recognizing that the TRR can 

vary among release groups based on differences in sampling effort, navailable was estimated for 

each release group as:
15

n n x t available released

(5)

where nreleased represents the total number of CWT juvenile Chinook salmon within a release 

group and t represents the fraction of time the Chipps Island Trawl Site was sampled from the 

first recovery to the last recovery of CWT juvenile Chinook salmon in the release group. The 

assumption of this approach is that juvenile Chinook salmon within a release group are equally 

distributed in time and have 100% survival.

A release group was defined as a group of CWT juvenile Chinook salmon that had the same 

hatchery origin and were released at the same location and time. A total of 74 releases have 

occurred at Sherman Island or Jersey Point from field seasons 1989 to 2011. All release groups 

at Sherman Island and Jersey Point were included in the calculation of 

TRR

to maximize sample 

size and obtain a more robust estimate. Fork lengths from the release groups ranged from 76 mm 

to 183 mm (mean = 93 mm), which covers the size range of the majority of unmarked juvenile 

Chinook salmon historically collected at Chipps Island. All release group data were obtained 

through the Regional Mark Information System (PSMFC 2012).

The

TRR

was calculated as an average of TRRs weighted by the number of individuals within 

each release group. To incorporate uncertainty in the estimated

TRR

, the monthly absolute 

abundance estimates were calculated using the 

TRR

and its 95% confidence limits. We calculated 

absolute abundance estimates from April to June during the 1978 through 2011 field seasons for 

fall-run Chinook salmon and calculated annual absolute abundance estimates during the 1995 

through 2011 field seasons for all races of Chinook salmon to reflect increases in sampling 

frequency throughout the field season at Chipps Island during the 1990s. 

River Flow Conditions

River flow data were obtained from the USGS and CDWR (USGS 2012; CDWR 2012a). We 

obtained mean daily discharge data at the Colusa (River Mile, RM 144) and Freeport (RM 48) 

gauging stations on the lower Sacramento River, and at the Vernalis (RM 114) gauging station

on the lower San Joaquin River to represent the primary flow inputs into the Estuary. Further, 

daily Delta outflow estimates were obtained from Dayflow (CDWR 2012a) to estimate discharge

past Chipps Island towards the San Francisco Bay, which takes into account water exports. We 

also obtained water year type classifications for the Sacramento and San Joaquin River basins 

from the California Data Exchange Center (CDWR 2012b). 

We presented the mean monthly CPUE of fishes of management concern along with mean 

monthly discharge during the 2010 and 2011 field seasons to examine species relationships with 

flow. Similarly, we compared the yearly CPUE of fishes of management concern along with 

mean yearly discharge at each trawl site and seine region. In addition, we related the mean 

weekly CPUE with mean weekly discharge for the 2010 and 2011 field seasons for fish species 

that appeared to have a distinct relationship to river discharge. The mean CPUE estimates of 

fishes of management concern within a seine region or trawl site were related to mean discharge

estimates thought to represent discharge within the trawl site and seine regions. Generally, the 

CPUE of fishes within the Lower Sacramento River Seine Region were related to discharge data 
16

measured at Colusa. The CPUE of fishes within the North Delta Seine Region and the 

Sacramento Trawl Site were related to discharge data measured at Freeport. The CPUE data 

from the Lower San Joaquin River Seine Region, South Delta Seine Region, Central Delta Seine 

Region, and the Mossdale Trawl Site were related to discharge data measured at Vernalis. 

Finally, the CPUE of fishes within the Chipps Island Trawl Site and San Francisco and San 

Pablo Bay Seine Region were related to estimated delta outflow (henceforth referred to as delta 

discharge) data. The mean weekly CPUE of each species of management concern were related to 

flow conditions only during months of occurrence within each seine region or trawl site to 

account for possible seasonal migration patterns. 

Water temperature data were also obtained from the USGS and CDWR to compliment available 

discharge data (USGS 2012; CDWR 2012b). We obtained daily maximum water temperature 

data from the Mallard Island gauging station during the 1989 to 2011 field seasons to represent 

the temperature of water exiting the Delta (CDWR 2012b). The Mallard Island gauging station is 

the only water station near the Chipps Island Trawl Site that provided continuous water 

temperature data prior to the 2000 field season. We also obtained daily maximum water 

temperature data from the Freeport and Vernalis gauging stations to represent the temperature of 

water entering the Delta from the Sacramento and San Joaquin rivers, respectively during the 

2000 to 2011 field seasons. Within this report, we calculated the mean maximum water 

temperature by month and field season.

RESULTS AND DISCUSSION

During the 2010 and 2011 field seasons, a total of 12,902 fish samples (e.g., seine hauls or trawl 

tows) were collected without any severe gear malfunctions and were included in our analysis. 

We completed 2,954 trawl tows at the Chipps Island Trawl Site, 3,441 trawls at the Mossdale 

Trawl Site, and 2,717 trawl tows at the Sacramento Trawl Site. The trawl tows were evenly 

distributed throughout the 2010 and 2011 field seasons (Tables A2 and A3). As a result, interand intra-annual trawl catch comparisons were considered robust due to minimal spatial and 

temporal bias. 

Conversely, there was considerable spatial and temporal variability in the number of samples 

collected at sites within nearly all seine regions during the 2010 and 2011 field seasons (Tables 

A4 - A17). For example, on average only approximately 50% and 53% of the historically 

sampled sites within the South Delta Seine Region were effectively sampled during sample 

weeks within the 2010 and 2011 field seasons, respectively (Tables A12 and A13). The number 

of samples collected within the South Delta Seine Region during the 2010 (n=256) and 2011 

(n=275) field season were considerably lower than the previous decade's annual average ( =329, 

SE=15.7). In addition, on average only approximately 31% and 26% of the historically sampled 

sites within the Lower San Joaquin Seine Region were effectively sampled during sample weeks 

within the 2010 and 2011 field seasons, respectively (Tables A14 and A15). The number of 

samples collected within the Lower San Joaquin River Seine Region during the 2010 (n=120) 

and 2011 (n=99) field season were considerably lower than the previous decade's annual average 

( =160, SE=4.88). As a result, catch data associated with these seine regions may contain both 

inter- and intra-annual bias. 
17

Throughout the 2010 and 2011 field seasons, the inability to effectively sample sites resulted 

from high tides, the expansion of submerged, emergent, and floating aquatic vegetation, and 

extreme river discharge (e.g., high and low). However, the Sacramento Area Seine Region 

appeared to be only sampled one day per week versus the traditional three days per week 

throughout the month of January during both the 2010 and 2011 field seasons (Tables A8 and 

A9) likely due to scheduling errors. The DJFMP is currently investigating the feasibility of 

implementing a stratified random sampling design for beach seining within the San Francisco 

Estuary or replacing problematic seine sites with suitable and adaptable replicates to reduce the 

impact of recent and growing inaccessibility to fixed sites within seine regions. New sampling 

methods or sites are needed to re-establish and ensure future continuity of non-biased

representative catch data.

Within this report, seine catch data were primarily used to evaluate the general temporal and 

spatial distribution patterns (i.e., occupancy) of fish within the San Francisco Estuary. Although 

the spatial and temporal variability of the samples collected within seine regions can affect 

occupancy patterns (e.g., discerning between false absences within regions; decreasing detection 

probability with fewer samples), the DJFMP seine catch data does successfully document the 

presence of fishes at a given time and location. However, detection probability and the 

probability of reporting false absences (present but not captured) remain unknown.

A total of 441,889 fishes, representing 77 different species, were captured during the 2010 and 

2011 field seasons (Table A18 and A19). Sixty-five percent (n=288,825) of the fishes were 

observed during the 2011 field season. Approximately 71% (n=109,279) and 41% (n=116,649) 

of the fishes captured during the 2010 and 2011 field seasons were identified as species not 

native to the San Francisco Estuary, respectively. A total of 5,428 fishes were unable to be 

accurately identified during the 2010 and 2011 field seasons. All unidentified fish were observed 

at the Mossdale Trawl Site during the period when the CDFG conducted sampling. Of the 77

species observed, the inland silverside (Menidia beryllina), Sacramento splittail, juvenile 

Chinook salmon, red shiner (Cyprinella lutrensis), Sacramento sucker (Catostomus occidentalis),

American shad (Alosa sapidissima), and threadfin shad comprised 84% and 87% of the total 

catch during the 2010 and 2011 field seasons, respectively. The Sacramento sucker was the most 

common species observed and comprised 25% (n=14,174) of all fishes captured in the Lower 

Sacramento River Seine Region (Region 1) during the 2010 and 2011 field seasons (Table A18 

and A19). Within the Lower San Joaquin River Seine Region (Region 5), the red shiner was the 

most common species observed and comprised 50% (n=24,616) of all fishes captured. The 

inland silverside was the most common species observed and comprised 58% (n=106,072) of all 

fishes captured in the North Delta (Region 2), Central Delta (Region 3), and South Delta (Region 

4) Seine regions. Within the San Francisco/San Pablo Bay Seine Region (Region 6), the top 

smelt (Atherinops affinis) was the most common fish species observed and comprised 60% 

(n=9,620) of all fishes captured. At the Chipps Island Trawl Site, the American shad was the 

most common species observed and comprised 52% (n=18,137) of the fishes captured during the 

2010 and 2011 field seasons. Conversely, the juvenile Chinook salmon and Sacramento splittail 

were the most common species captured at the Sacramento and Mossdale Trawl sites, 

respectively. 
18

The higher proportion of native fishes observed during the 2011 field season relative to the 2010 

field season may have resulted, in part, from higher recruitment of a few native fishes (i.e., 

Sacramento splittail and Chinook salmon) in response to higher in-river flows and cooler water 

temperatures within the San Francisco Estuary and its watershed. The water year classification 

index for 2011 was identified as "wet" within both the Sacramento and San Joaquin River basins. 

Conversely, the index for 2010 was identified as below normal and above normal within the

Sacramento and San Joaquin River basins, respectively. Indices from 2007 to 2009 were also 

generally identified as "dry" or "critically dry" (Table A20; CDWR 2012b). In addition, the 

mean maximum water temperatures were, on average, lower during the months of February

through June within the entry and exit points of the Delta during the 2011 field season relative to 

the 2010 field season (Tables A21-A23). Because the majority of the non-native fishes observed 

by the DJFMP are considered warm water species originating from the Mississippi River Basin 

(Tables A18 and A19; Moyle 2002), the aquatic habitats occurring within the San Francisco 

Estuary and the lower Sacramento and San Joaquin rivers were likely less optimal for non-native 

species in terms of spawning or rearing during the 2011 field season relative to native species.

Chinook salmon

We captured 11,389 and 20,556 juvenile Chinook salmon during the 2010 and 2011 field 

seasons, respectively (Tables A18 and A19). During the 2010 field season, 8,514 individuals 

were unmarked and 1.7% (n=145) were identified as winter-run, 83.6% (n=7,119) were 

identified as fall-run, 14% (n=1,194) were identified as spring-run, and less than 1% (n=56) were 

identified as late fall-run (Table A18). Of the 2,875 marked juvenile Chinook salmon recovered 

during 2010, 97% (n=2,791) contained a CWT (Table A24). During the 2011 field season, 

18,451 individuals were unmarked and 1.5% (n=280) were identified as winter-run, 87.4% 

(n=16,117) were identified as fall-run, 10.9% (n=2,002) were identified as spring-run, and less 

than 1% (n=52) were identified as late fall-run Chinook salmon (Table A19). Of the 2,105

marked juvenile Chinook salmon recovered during 2011, 94% (n=1,984) contained a CWT

(Table A25). 

During the 2010 and 2011 field seasons, marked juvenile winter-run Chinook salmon containing 

a CWT were recovered by the DJFMP within the Lower Sacramento River Seine Region, the 

Sacramento Trawl Site, and the Chipps Island Trawl Site (Tables A24 and A25). All recovered 

CWT winter-run Chinook salmon were released by the Livingston Stone National Fish Hatchery

which tagged and released 792,962 and 123,870 CWT juveniles during the 2010 and 2011 field 

seasons, respectively (PSMFC 2012). Marked juvenile spring-run Chinook salmon were 

recovered within the Lower Sacramento River and North Delta Seine regions, the Sacramento 

Trawl Site, and the Chipps Island Trawl Site during the 2010 and 2011 field seasons (Tables A24 

and A25). All recovered CWT spring-run Chinook salmon were released by the Feather River 

Fish Hatchery which tagged and released 2,126,054 and 2,312,010 CWT juveniles during the 

2010 and 2011 field seasons, respectively (PSMFC 2012). Marked juvenile fall-run Chinook 

salmon containing a CWT were recovered within the Lower Sacramento River, North Delta, 

Central Delta, Lower San Joaquin River, and Sacramento Area Seine regions, the Sacramento 

Trawl Site, the Mossdale Trawl Site, and the Chipps Island Trawl Site (Tables A24 and A25). In 

the 2010 field season, 17,828,674 CWT juvenile fall-run Chinook salmon were released in the 

combined release efforts of the Coleman National Fish Hatchery (16%), Feather River Fish 
19

Hatchery (46%), Mokelumne River Fish Hatchery (11%), Nimbus Fish Hatchery (26%), and 

Merced River Fish Facility (1%; PSMFC 2012). In the 2011 field season, 9,244,498 CWT 

juvenile fall-run Chinook salmon were released in the combined release efforts of the Coleman 

National Fish Hatchery (35%), Feather River Fish Hatchery (31%), Nimbus Fish Hatchery 

(15%), and Merced River Fish Facility (1%; PSMFC 2012). During the 2010 and 2011 field 

seasons, marked juvenile late fall-run Chinook salmon containing a CWT were recovered within 

the Lower Sacramento River, North Delta, Central Delta, and Sacramento Area Seine regions, 

the Sacramento Trawl Site, and the Chipps Island Trawl Site (Tables A24 and A25). All 

recovered CWT late fall-run Chinook salmon were found to be released by the Coleman National 

Fish Hatchery which tagged and released a total of 1,154,761 and 1,011,972 CWT juveniles 

during the 2010 and 2011 field seasons, respectively (PSMFC 2012). During the 2010 field 

season, the Federal and State Fish facilities recovered 29 winter-run, eight fall-run, and 313 late 

fall-run CWT juvenile Chinook salmon (Table A24). Therefore, based on CWT recoveries by the 

DJFMP and fish facilities during the 2010 and 2011 field seasons, there is evidence that races 

specific to the Sacramento River Basin (e.g., winter-, spring-, and late fall-run) can occur within 

the Central and South Delta likely based on water diversions, exports, and tides. As a result, 

CWT recovery data further validates our application of the size at date of capture river criteria to 

identify the race of unmarked juvenile Chinook salmon captured in all seine regions with the 

exception of the Lower San Joaquin River Seine Region. 

Unmarked Winter-Run Distribution and Relative Abundance

Unmarked juvenile winter-run Chinook salmon were captured in relatively low numbers within 

in the Lower Sacramento River, North Delta, Central Delta, and Sacramento Area Seine regions, 

the Sacramento Trawl Site, and the Chipps Island Trawl Site during the 2010 and 2011 field 

seasons (Tables A18 and A19). Individuals were generally captured from January through April 

at the Chipps Island Trawl Site and October through April at the Sacramento Trawl Site (Figures 

7 and 8). The CPUE at the Sacramento Trawl Site peaked in February and December during the 

2010 and 2011 field seasons, respectively. Conversely, the CPUE at the Chipps Island Trawl Site 

peaked in March and April during the 2010 and 2011 field seasons, respectively. Because there 

was generally a one to three month time lag in the first detection or peak CPUE of winter-run at 

the Sacramento and Chipps Island Trawl sites during both field seasons, there is evidence that 

unmarked juvenile winter-run may rear within the Sacramento and San Joaquin Delta for several 

weeks, which is similar to other runs within the Estuary (Kjelson et al. 1982). The mean yearly 

CPUE at the Sacramento and Chipps Island Trawl sites were near record lows during both the 

2010 and 2011 field seasons (Figures 7 and 8).

In beach seines, unmarked juvenile winter-run Chinook salmon were detected in most months 

from October through April during the 2010 and 2011 field seasons (Figure 9). Mean monthly 

CPUE peaked in the Lower Sacramento River, North Delta, and Central Delta Seine regions 

during the month of January and December during the 2010 and 2011 field seasons, respectively. 

However, only two and one fish were captured within the Central Delta Seine Region during the 

2010 and 2011 field seasons, respectively. The mean yearly CPUE estimates suggest that 

unmarked juvenile winter-run Chinook salmon were consistently observed in higher densities 

within the Lower Sacramento River Seine Region relative to other seine regions since the 2000 

field season (Figure 9). Similar to the Sacramento Trawl Site, unmarked winter-run Chinook
20

salmon were first detected within the Sacramento Area Seine Region near the Delta Cross 

Channel water diversion gates during the month of October for both the 2010 and 2011 field 

seasons (Figure 10). 

 

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

0.00

0.02

0.04

0.06

0.08

0.10

0.12

0

200

400

600

800

1000

a) Winter-run

n = 69

2010

X Data

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

CPUE (fish/10,000 m

3

)

0.00

0.02

0.04

0.06

0.08

0.10

0.12

Mean Discharge (m

3/sec)

0

1000

2000

3000

4000

b) Winter-run

n = 64

2011

1996 1998 2000 2002 2004 2006 2008 2010

0.00

0.02

0.04

0.06

0.08

0.10

0

300

600

900

1200

1500

1800

c) Winter-run

Inter-Annual

Figure 7. Mean monthly and yearly CPUE (bars) of unmarked juvenile winter-run Chinook 

salmon captured in mid-water trawls (MWTRs) at the Chipps Island Trawl Site and mean 

monthly and yearly Delta discharges (lines) during the a) 2010, b) 2011, and c) 1995 through 

2011 field seasons. Sample size (n) corresponds to total number of fish caught.
21

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

0.00

0.01

0.02

0.03

0.04

0.05

0.06

0.07

0

200

400

600

800

1000 a) Winter-run

2010

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

CPUE (fish/10,000 m

3

)

0.00

0.02

0.04

0.06

0.08

0.10

0.12

Mean Discharge (m

3/sec)

0

400

800

1200

1600

2000

b) Winter-run

2011

2000 2002 2004 2006 2008 2010

0.00

0.05

0.10

0.15

0.20

0.25

0

200

400

600

800

1000

1200

MWTR, n = 0

KDTR, n = 13

c) Winter-run

Inter-Annual

MWTR, n = 5

KDTR, n = 15

Figure 8. Mean monthly and yearly CPUE (bars) of unmarked juvenile winter-run Chinook 

salmon captured in mid-water (MWTRs) and Kodiak trawls (KDTRs) at the Sacramento Trawl 

Site and mean monthly Sacramento River discharge at Freeport (lines) during the a) 2010, b) 

2011, and c) 2000 through 2011 field seasons. Sample size (n) corresponds to total number of 

fish caught.
22

Figure 9. Mean monthly and yearly CPUE of unmarked juvenile winter-run Chinook salmon 

captured in beach seines at regions one through six, and mean monthly and yearly Sacramento 

River discharge at Freeport, San Joaquin River discharge at Vernalis, and Delta discharge during 

the a) 2010, b) 2011, and c) 2000 through 2011 field seasons. Sample size (n) corresponds to 

total number of fish caught.

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

0

50

100

150

200

250

0

200

400

600

800

1000 a) Winter-run

n = 41

2010

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

CPUE (fish/10,000 m

3

)

0

200

400

600

800

1000

1200

Mean Discharge (m

3/sec)

0

600

1200

1800

2400

3000

3600

2001 2003 2005 2007 2009 2011

0

100

200

300

400

0

300

600

900

1200

1500

1800

Region 1

Region 2

Region 3

Region 4

Delta Outflow

Vernalis

Freeport

b) Winter-run

n = 169

2011

c) Winter-run

Inter-Annual
23

X Data

Oct Nov Dec Jan Feb 

0

30

60

90

120

150

180

0

300

600

900

1200

1500

1800 a) Winter-run

n = 34

2010

X Data

Oct Nov Dec Jan Feb 

CPUE (fish/10,000 m

3

)

0

500

1000

1500

2000

2500

Mean Discharge (m

3/sec)

0

400

800

1200

1600

2000

2400 b) Winter-run

n = 126

2011

2000 2002 2004 2006 2008 2010

0

100

200

300

400

500

0

200

400

600

800

1000 c) Winter-run

Inter-Annual

Figure 10. Mean weekly and yearly CPUE (bars) of unmarked juvenile winter-run Chinook 

salmon captured in beach seines at the Sacramento Area Seine (Region 7), and mean weekly and 

yearly Sacramento River discharge at Freeport (lines) from October to January during the a) 

2010, b) 2011, and c) 2000 through 2011 field seasons. Sample size (n) corresponds to total 

number of fish caught.

Unmarked Fall-Run Distribution and Relative Abundance

Unmarked juvenile fall-run Chinook salmon were captured in nearly all seine regions and trawl 

sites during the 2010 and 2011 field seasons (Tables A18 and A19). However, no individuals 

were captured within the Lower San Joaquin Seine Region during the 2011 field season. At the 

Chipps Island Trawl Site, individuals were captured from March through October and the largest

mean monthly CPUE estimates were observed from April through June (Figure 11). Individuals 

were generally captured from January through July at the Sacramento Trawl Site during both 
24

field seasons, but individuals also were observed in relatively high densities in the month of 

December during the 2011 field season (Figure 12). At the Mossdale Trawl Site, unmarked 

juvenile fall-run Chinook salmon were primarily captured from February through July during 

both field seasons, but individuals also were observed in relatively low densities from November 

through January during the 2011 field season (Figure 13). Therefore, it appears that the period of 

immigration of unmarked juvenile fall-run Chinook salmon into the San Francisco Estuary from 

both the San Joaquin and Sacramento River basins was earlier and longer in 2011 than 2010.

The mean monthly CPUE at all three trawl sites peaked either in April or May during both field 

seasons. 

The mean yearly CPUE at the Chipps Island Trawl Site has increased annually since the record 

low observed during the 2008 field season (Figure 11). In addition, the 2011 mean yearly April 

through June CPUE estimate (4.75 fish/10,000m3) did exceed the 1978 to 2009 average (4.62 

fish/10,000m3; Figure 14). The mean yearly CPUE at the Mossdale Trawl Site was the lowest 

during 2010 and was a record high during 2011 since the 2004 field season (Figure 13). 

Similarly, the mean yearly CPUE at the Sacramento Trawl Site was the lowest in 2010 since the 

2000 field season and increased slightly during the 2011 field season (Figure 12). 

In terms of beach seine monitoring, unmarked juvenile fall-run Chinook salmon were detected in

months from December to June during the 2010 and 2011 field seasons (Figure 15). The mean 

monthly CPUE peaked in the Lower Sacramento River, North Delta, and Central Delta Seine 

regions during the months of January and February, whereas the mean monthly CPUE generally 

peaked in the Lower San Joaquin River and South Delta Seine regions during the months of 

February and March (Figure 15). Within the San Francisco/San Pablo Bay Seine Region, mean 

monthly CPUE peaked during the month of May during both field seasons, however only a total 

of one and four individuals were captured during the 2010 and 2011 field seasons, respectively. 

The mean yearly CPUE estimates suggest that unmarked juvenile fall-run Chinook salmon were 

observed in higher densities particularly within the Lower Sacramento River, North Delta, and 

Central Delta Seine regions relative to other seine regions since the 2000 field season. Densities 

within these regions have increased annually since the record low was observed in 2009 (Figure 

15).
25

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

0.00

0.04

0.08

1.00

2.00

3.00

4.00

5.00

0

200

400

600

800

1000

a) Fall-run

n = 2,430

2010

X Data

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

CPUE (fish/10,000 m

3

)

0.0

0.1

2.0

4.0

6.0

8.0

Mean Discharge (m

3/sec)

0

1000

2000

3000

4000

b) Fall-run

n = 3,570

2011

1996 1998 2000 2002 2004 2006 2008 2010

0.0

0.5

1.0

1.5

2.0

2.5

0

300

600

900

1200

1500

1800

c) Fall-run

Inter-Annual

Figure 11. Mean monthly and yearly CPUE (bars) of unmarked juvenile fall-run Chinook salmon 

captured in mid-water trawls (MWTRs) at the Chipps Island Trawl Site and mean monthly and 

yearly Delta discharges (lines) during the a) 2010, b) 2011, and c) 1995 through 2011 field 

seasons. Sample size (n) corresponds to total number of fish caught.
26

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

0

200

400

600

800

1000

0

2

4

6

8

a) Fall-run

2010

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

CPUE (fish/10,000 m

3

)

0

2

4

6

8

10

12

Mean Discharge (m

3/sec)

0

400

800

1200

1600

2000

b) Fall-run

2011

2000 2002 2004 2006 2008 2010

0

5

10

15

20

25

0

200

400

600

800

1000

1200

MWTR, n = 1,273

KDTR, n = 461

c) Fall-run

Inter-Annual

MWTR, n = 457

KDTR, n = 258

Figure 12. Mean monthly and yearly CPUE (bars) of unmarked juvenile fall-run Chinook salmon 

captured in mid-water (MWTRs) and Kodiak trawls (KDTRs) at the Sacramento Trawl Site and 

mean monthly Sacramento River discharge at Freeport (lines) during the a) 2010, b) 2011, and c) 

2000 through 2011 field seasons. Sample size (n) corresponds to total number of fish caught.
27

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

0.0

0.2

0.4

0.6

0.8

1.0

0

30

60

90

120

150 a) Fall-run

n = 296

2010

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

CPUE (fish/10,000 m

3

)

0

2

4

6

8

10

Mean Discharge (m

3/sec)

0

200

400

600

800

2004 2005 2006 2007 2008 2009 2010 2011

0.0

0.5

1.0

1.5

2.0

2.5

3.0

0

75

150

225

300

b) Fall-run

n = 3,235

2011

c) Fall-run

Inter-Annual

Figure 13. Mean monthly and yearly CPUE (bars) of unmarked juvenile fall-run Chinook salmon 

captured in Kodiak trawls (KDTRs) at the Mossdale Trawl Site and mean monthly and yearly 

San Joaquin River discharge at Vernalis (lines) during the a) 2010, b) 2011, and c) 2004 through 

2011 field seasons. Sample size (n) corresponds to total number of fish caught.
28

1980 1985 1990 1995 2000 2005 2010

CPUE (fish/10,000 m

3

)

0

2

4

6

8

10

12

Mean Discharge (m

3/sec)

0

500

1000

1500

2000

2500

3000

Figure 14. Mean CPUE (bars) of unmarked juvenile fall-run Chinook salmon captured in midwater trawls (MWTRs) at the Chipps Island Trawl Site and mean Delta discharges (line) during 

April through June from the 1978 to 2011 field seasons. 
29

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

0

2000

4000

6000

8000

10000

12000

0

200

400

600

800

1000 a) Fall-run

n = 3,678

2010

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

CPUE (fish/10,000 m

3

)

0

3000

6000

9000

12000

15000

18000

21000

Mean Discharge (m

3/sec)

0

600

1200

1800

2400

3000

3600

2001 2003 2005 2007 2009 2011

0

1000

2000

3000

4000

5000

6000

7000

0

300

600

900

1200

1500

1800

Region 1

Region 2

Region 3

Region 4

Region 5

Region 6

Delta Outflow

Vernalis

Freeport

b) Fall-run

n = 7,354

2011

c) Fall-run

Inter-Annual

Figure 15. Mean monthly and yearly CPUE of unmarked juvenile fall-run Chinook salmon 

captured in beach seines at regions one through six, and mean monthly and yearly Sacramento 

River discharge at Freeport, San Joaquin River discharge at Vernalis, and Delta discharge during 

the a) 2010, b) 2011, and c) 2000 through 2011 field seasons. Sample size (n) corresponds to 

total number of fish caught.

Unmarked Spring-Run Distribution and Relative Abundance

Unmarked juvenile spring-run Chinook salmon were captured in the Lower Sacramento River, 

North Delta, Central Delta, and South Delta Seine regions, the Sacramento Trawl Site, and the 

Chipps Island Trawl Site during the 2010 and 2011 field seasons (Tables A18 and A19).

Additionally, one individual was captured in the San Francisco/San Pablo Bay Seine Region 

during the 2011 field season. At the Chipps Island Trawl Site, individuals were primarily 

captured from March through May during both field seasons, and during the month of June 

during the 2011 field season (Figure 16). Individuals were generally captured from January
30

through May at the Sacramento Trawl Site (Figure 17). The mean monthly CPUE at the 

Sacramento and Chipps Island Trawl sites peaked strongly in April during the 2010 and 2011 

field seasons, suggesting a short residence time within the Delta. The mean yearly CPUE at the 

Chipps Island and Sacramento Trawl sites increased during the 2010 and 2011 field seasons from 

near record lows observed in 2008 (Figures 16 and 17). 

In beach seines, unmarked juvenile spring-run Chinook salmon were detected during the months 

of December through April and October through May during the 2010 and 2011 field seasons, 

respectively (Figure 18). The mean monthly CPUE peaked in the Lower Sacramento River, 

North Delta, and Central Delta Seine regions within the 2010 field season during February 

through April. In contrast, the mean monthly CPUE generally peaked in the same regions during

the 2011 field season in January and February (Figure 18). Within the South Delta Seine Region, 

unmarked juvenile spring-run Chinook salmon were detected in very low numbers in March 

(n=1) during the 2010 field season, and April and May (n=4) during the 2011 field season. The 

mean yearly CPUE estimates suggest that unmarked juvenile spring-run Chinook salmon were 

consistently observed in higher densities within the Lower Sacramento River and North Delta 

Seine regions relative to other seine regions since the 2000 field season. Densities within these 

regions have increased annually since a near record low was observed in 2008 and 2009 (Figure 

18). Unmarked spring-run Chinook salmon were first detected within the Sacramento Area Seine 

Region near the Delta Cross Channel water diversion gates during late December and early 

November for the 2010 and 2011 field seasons, respectively (Figure 19). 
31

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

0.0

0.5

1.0

1.5

2.0

2.5

0

200

400

600

800

1000 a) Spring-run

n = 757

2010

X Data

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

CPUE (fish/10,000 m

3

)

0.0

0.4

0.8

1.2

1.6

2.0

Mean Discharge (m

3/sec)

0

1000

2000

3000

4000

b) Spring-run

n = 594

2011

1996 1998 2000 2002 2004 2006 2008 2010

0.0

0.2

0.4

0.6

0.8

0

300

600

900

1200

1500

1800 c) Spring-run

Inter-Annual

Figure 16. Mean monthly and yearly CPUE (bars) of unmarked juvenile spring-run Chinook 

salmon captured in mid-water trawls (MWTRs) at the Chipps Island Trawl Site and mean 

monthly and yearly Delta discharges (lines) during the a) 2010, b) 2011, and c) 1995 through 

2011 field seasons. Sample size (n) corresponds to total number of fish caught.
32

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

0.0

0.5

1.0

1.5

2.0

2.5

3.0

0

200

400

600

800

1000 a) Spring-run

2010

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

CPUE (fish/10,000 m

3

)

0

1

2

3

4 Mean Discharge (m

3/sec)

0

400

800

1200

1600

2000

b) Spring-run

2011

2000 2002 2004 2006 2008 2010

0.0

0.5

1.0

1.5

2.0

0

200

400

600

800

1000

1200

MWTR, n = 153

KDTR, n = 16

c) Spring-run

Inter-Annual

MWTR, n = 277

KDTR, n = 73

Figure 17. Mean monthly and yearly CPUE (bars) of unmarked juvenile spring-run Chinook 

salmon captured in mid-water (MWTRs) and Kodiak trawls (KDTRs) at the Sacramento Trawl 

Site and mean monthly Sacramento River discharge at Freeport (lines) during the a) 2010, b) 

2011, and c) 2000 through 2011 field seasons. Sample size (n) corresponds to total number of 

fish caught.
33

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

0

200

400

600

800

1000

0

100

200

300

400

500

600

700 a) Spring-run

n = 268

2010

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

CPUE (fish/10,000 m

3

)

0

300

600

900

1200

1500

1800

Mean Discharge (m

3/sec)

0

600

1200

1800

2400

3000

3600

2001 2003 2005 2007 2009 2011

0

100

200

300

400

500

0

300

600

900

1200

1500

1800

Region 1

Region 2

Region 3

Region 4

Region 6

Delta Outflow

Vernalis

Freeport

b) Spring-run

n = 1,022

2011

c) Spring-run

Inter-Annual

Figure 18. Mean monthly and yearly CPUE of unmarked juvenile spring-run Chinook salmon 

captured in beach seines at regions one through six, and mean monthly and yearly Sacramento 

River discharge at Freeport, San Joaquin River discharge at Vernalis, and Delta discharge during 

the a) 2010, b) 2011, and c) 2000 through 2011 field seasons. Sample size (n) corresponds to 

total number of fish caught.
34

X Data

Oct Nov Dec Jan Feb 

0

30

60

90

120

150

180

0

300

600

900

1200

1500

1800 a) Spring-run

n = 13

2010

X Data

Oct Nov Dec Jan Feb 

CPUE (fish/10,000 m

3

)

0

500

1000

1500

2000

2500

3000

Mean Discharge (m

3/sec)

0

400

800

1200

1600

2000

2400 b) Spring-run

n = 307

2011

2000 2002 2004 2006 2008 2010

0

100

200

300

400

500

600

700

0

200

400

600

800

1000 c) Spring-run

Inter-Annual

Figure 19. Mean weekly and yearly CPUE (bars) of unmarked juvenile spring-run Chinook 

salmon captured in beach seines at the Sacramento Area Seine (Region 7), and mean weekly and 

yearly Sacramento River discharge at Freeport (lines) from October to January during the a) 

2010, b) 2011, and c) 2000 through 2011 field seasons. Sample size (n) corresponds to total 

number of fish caught.

Unmarked Late Fall-Run Distribution and Relative Abundance

We captured low numbers of unmarked juvenile late fall-run Chinook salmon in the Lower 

Sacramento River and North Delta Seine regions, the Sacramento Trawl Site, and the Chipps 

Island Trawl Site during the 2010 and 2011 field seasons (Tables A18 and A19). Four 

individuals also were detected in the Central Delta Seine Region during the 2010 field season.

Individuals were generally detected in months from September through January at the Chipps 

Island Trawl Site and August through December at the Sacramento Trawl Site (Figures 20 and
35

21). The mean monthly CPUE at the Chipps Island Trawl Site peaked in January and December 

during the 2010 and 2011 field seasons, respectively. Because of the relatively few detections 

combined with low catches per month (n=1), no discernible peaks in mean monthly CPUE can 

be identified at the Sacramento Trawl Site during either field season. The mean yearly CPUE at 

the Chipps Island and Sacramento Trawl sites were near record lows during both the 2010 and 

2011 field seasons (Figures 20 and 21). 

Unmarked juvenile late fall-run Chinook salmon were generally detected in low numbers in 

beach seines from October through January and April through May during both the 2010 and 

2011 field seasons (Figure 22), suggesting a bimodal distribution as a result of two distinct age 

classes. However, no individuals were detected in the Lower Sacramento River Seine Region in

the spring during the 2011 field season. The mean yearly CPUE estimates also suggest that 

unmarked juvenile late fall-run Chinook salmon were consistently observed in higher densities 

within the Lower Sacramento River and North Delta Seine regions relative to other seine regions 

since the 2000 field season. Densities within these regions have increased annually since a near 

record low was observed in 2008 and 2009 (Figure 22).
36

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

0.000

0.005

0.010

0.015

0.020

0.025

0

200

400

600

800

1000 a) Late fall-run

n = 11

2010

X Data

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

CPUE (fish/10,000 m

3

)

0.000

0.004

0.008

0.012

0.016

Mean Discharge (m

3/sec)

0

1000

2000

3000

4000

b) Late fall-run

n = 13

2011

1996 1998 2000 2002 2004 2006 2008 2010

0.00

0.01

0.02

0.03

0.04

0

300

600

900

1200

1500

1800 c) Late fall-run

Inter-Annual

Figure 20. Mean monthly and yearly CPUE (bars) of unmarked juvenile late fall-run Chinook 

salmon captured in mid-water trawls (MWTRs) at the Chipps Island Trawl Site and mean 

monthly and yearly Delta discharges (lines) during the a) 2010, b) 2011, and c) 1995 through 

2011 field seasons. Sample size (n) corresponds to total number of fish caught.
37

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

0.000

0.003

0.006

0.009

0.012

0.015

0

200

400

600

800

1000 a) Late fall-run

2010

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

CPUE (fish/10,000 m

3

)

0.000

0.004

0.008

0.012

0.016

0.020

Mean Discharge (m

3/sec)

0

400

800

1200

1600

2000

b) Late fall-run

2011

2000 2002 2004 2006 2008 2010

0.00

0.01

0.02

0.03

0.04

0

200

400

600

800

1000

1200

MWTR, n = 1

KDTR, n = 1

c) Late fall-run

Inter-Annual

MWTR, n = 1

KDTR, n = 2

Figure 21. Mean monthly and yearly CPUE (bars) of unmarked juvenile late fall-run Chinook 

salmon captured in mid-water (MWTRs) and Kodiak trawls (KDTRs) at the Sacramento Trawl 

Site and mean monthly Sacramento River discharge at Freeport (lines) during the a) 2010, b) 

2011, and c) 2000 through 2011 field seasons. Sample size (n) corresponds to total number of 

fish caught.
38

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

0

30

60

90

120

150

180

0

200

400

600

800

a) Late fall-run 1000

n = 42

2010

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

CPUE (fish/10,000 m

3

)

0

20

40

60

80

100

120

140

Mean Discharge (m

3/sec)

0

600

1200

1800

2400

3000

3600

2001 2003 2005 2007 2009 2011

0

10

20

30

40

50

60

70

0

300

600

900

1200

1500

1800

Region 1

Region 2

Region 3

Region 4

Delta Outflow

Vernalis

Freeport

b) Late fall-run

n = 35

2011

c) Late fall-run

Inter-Annual

Figure 22. Mean monthly and yearly CPUE of unmarked juvenile late fall-run Chinook salmon 

captured in beach seines at regions one through six, and mean monthly and yearly Sacramento 

River discharge at Freeport, San Joaquin River discharge at Vernalis, and Delta discharge during 

the a) 2010, b) 2011, and c) 2000 through 2011 field seasons. Sample size (n) corresponds to 

total number of fish caught.

Influence of River Discharge

During the 2010 and 2011 field seasons, the mean CPUE of all unmarked juvenile Chinook 

salmon races generally peaked, particularly at the trawl sites and the Lower Sacramento River 

and North Delta Seine regions, during an increase in mean river discharge at nearly all temporal 

scales (i.e., weeks, months, and years; Figures 11 - 22). To examine these correlations, we 

developed simple linear regression models of mean weekly CPUE against log10 of the weekly 

mean river discharge data for each Chinook salmon race at the Chipps Island Trawl Site (Figure 

23), Sacramento Trawl Site (Figure 24), Mossdale Trawl Site (Figure 25), the Lower Sacramento 
39

Seine Region (Figure 26), and the North Delta Seine Region (Figure 27) during periods of 

occurrence in the 2010 and 2011 field seasons. Models were only developed during periods 

when Chinook salmon were captured in the 2010 and 2011 field seasons. Data for the 2010 and 

2011 seasons were grouped to examine a broad range of discharge values with 2011 

demonstrating greater discharge relative to the 2010 field season (Table A20; CDWR 2012b). 

The mean weekly CPUE of unmarked juvenile winter-, fall-, spring-, and late fall-run Chinook 

salmon during the 2010 and 2011 field seasons was consistently positively correlated with

transformed (log10) mean weekly river discharge. However, model results were generally weak 

and inconclusive (p-value > 0.05). For unmarked juvenile winter-run Chinook salmon, the 

proportion of mean weekly CPUE variability explained by river discharge ranged from 12% to 

23% among trawl sites and seine regions. The strongest correlation was observed at the

Sacramento Trawl Site with approximately 23% (n = 60, p-value = 0.05) of the variability in the 

mean weekly CPUE from October to April explained by the mean Sacramento River discharge at 

Freeport (Figure 24a). For unmarked juvenile fall-run Chinook salmon, the proportion of mean 

weekly CPUE variability explained by river discharge ranged from 11% to 36%. The strongest 

correlation was observed within the North Delta Seine Region with 36% (n = 60, p-value < 0.01) 

of the variability in catch from December to June explained by the Sacramento River discharge 

at Freeport (Figure 27b). For unmarked juvenile spring-run Chinook salmon, the proportion of 

mean weekly CPUE variability explained by river discharge ranged from 15% to 41%. The 

strongest correlation also was observed within the North Delta Seine Region (r2= 0.41, n = 42, 

p-value < 0.01; Figure 27c). For unmarked juvenile late fall-run Chinook salmon, the proportion 

of mean weekly CPUE variability explained by river discharge ranged from 11% to 19% among 

the Chipps Island Trawl Site and Lower Sacramento River and North Delta Seine regions. The

strongest correlation was observed at the Chipps Island Trawl Site with approximately 19% (n = 

44, p-value = 0.04) of the variability in catch explained by the mean weekly Delta discharge 

(Figure 23d). A negative correlation was observed between the mean weekly CPUE at the 

Sacramento Trawl Site and the mean Sacramento River discharge at Freeport from August 

through December (Figure 24d). However, the regression was based on the capture of only five 

individuals and was therefore not considered robust. 

Although the models were largely inconclusive for 2010 and 2011, the results consistently 

demonstrated a positive correlation between catch rates and discharge during periods of juvenile 

Chinook salmon occurrence within the San Francisco Estuary. Consequently, peaks in river 

discharge likely contributed to the earlier months of occupancy and higher relative abundances 

observed at most trawl sites and within seine regions during the 2011 field season compared to 

the 2010 field season. Our results are consistent with other investigations that have demonstrated 

that river discharge and/or water temperature (often correlated) are factors influencing the 

movement and abundance of juvenile Chinook salmon within the San Francisco Estuary (Kjelson 

et al. 1982; Stevens and Miller 1983; Kjelson and Brandes 1989; Kope and Botsford 1990; 

Brandes and McLain 2001; Jager and Rose 2003). Brandes and McLain (2001) analyzed 

historical DJFMP data and found that high Sacramento River discharges likely increased both

the movement and survival of fry sized (<70 mm in FL) juvenile Chinook salmon through the 

Estuary. In addition, Newman (2003) utilized a variety of modeling approaches in combination 

with DJFMP data and confirmed that river discharge and temperature were among the most 
40

influential predictors of hatchery reared juvenile Chinook salmon survival (i.e., catch) through 

the San Francisco Estuary. 

Despite the results from the present study, there is considerable uncertainty regarding if the 

increase in the relative abundance of unmarked juvenile Chinook salmon during periods of high 

river discharge reflects active or passive dispersal (Williams 2006). For example, fry may simply 

be involuntarily swept downstream into and through portions of the Estuary during periods of 

high discharge. Alternatively, higher river discharge may directly or indirectly improve aquatic 

habitats that are utilized by individuals to fulfill one or more of their life cycle requirements. 

Despite the evidence that river discharge does influence the relative abundance and distribution 

of unmarked juvenile Chinook salmon within the San Francisco Estuary, the importance of river 

discharge relative to water quality (e.g., contaminants, temperature, turbidity, salinity, etc.), other 

physical habitat characteristics (e.g., water current, floodplain availability, etc.), predation rates, 

innate cues (e.g., endogenous rhythms, celestial, etc.), and their interactions is still debated 

among researchers (e.g., Williams 2006; Zeug and Cavallo 2012). As a result, during the 2012 

field season the DJFMP initiated consistent data collection of several environmental variables 

hypothesized to influence the movement or survival of juvenile Chinook salmon to more 

properly assess the influence of water operations within the San Francisco Estuary.
41 2.0 2.2 2.4 2.6 2.8 3.0 3.2 3.4 3.6 3.8 4.0

0.000

0.075

0.150

0.225

0.300 a) Winter-run

r

2

 = 0.16

p-value = 0.16

2.0 2.2 2.4 2.6 2.8 3.0 3.2 3.4 3.6 3.8 4.0

CPUE (fish/10,000 m

3

)

0

5

10

15

20 b) Fall-run

r

2

 = 0.12

p-value = 0.16

2.2 2.4 2.6 2.8 3.0 3.2 3.4 3.6 3.8

0

2

4

6

8 c) Spring-run

r

2

 = 0.18

p-value = 0.11

Log10(Mean Discharge (m3/sec))

1.8 2.0 2.2 2.4 2.6 2.8 3.0 3.2 3.4 3.6

0.00

0.02

0.04

0.06

2010

2011

d) Late fall-run

r

2

 = 0.19

p-value = 0.04

Figure 23. Linear regressions of mean weekly CPUE of unmarked juvenile a) winter-, b) fall-, c) 

spring-, and d) late fall-run juvenile Chinook salmon captured in mid-water trawls (MWTRs) at 

the Chipps Island Trawl Site and concurrent mean weekly Delta discharges from a) JanuaryApril, b) March-July, c) March-June, and d) September-January during the 2010 and 2011 field 

seasons. 
42 2.2 2.4 2.6 2.8 3.0 3.2 3.4 3.6

0.000

0.075

0.150

0.225

0.300 a) Winter-run

r

2

 = 0.23

p-value = 0.05

2.2 2.4 2.6 2.8 3.0 3.2 3.4 3.6

CPUE (fish/10,000 m

3

)

0

5

10

15

20

25 b) Fall-run

r

2

 = 0.19

p-value = 0.07

2.2 2.4 2.6 2.8 3.0 3.2 3.4 3.6

0

4

8

12

16 c) Spring-run

r

2

 = 0.15

p-value = 0.40

Log10(Mean Discharge (m3/sec))

2.2 2.4 2.6 2.8 3.0 3.2 3.4

0.00

0.02

0.04

0.06

0.08 d) Late fall-run

r

2

 = 0.14

p-value = 0.55

MWTR 2010

KDTR 2010

MWTR 2011

KDTR 2011

Figure 24. Linear regressions of mean weekly CPUE of unmarked juvenile a) winter-, b) fall-, c) 

spring-, and d) late fall-run juvenile Chinook salmon captured in mid-water (MWTRs) and 

Kodiak trawls (KDTRs) at the Sacramento Trawl Site and mean weekly Sacramento River 

discharge at Freeport from a) October-April, b) December-July, c) December-May, and d) 

August-December during the 2010 and 2011 field seasons.
43

Log10(Mean Discharge (m3/sec))

1.4 1.6 1.8 2.0 2.2 2.4 2.6 2.8 3.0

CPUE (fish/10,000 m

3

)

0

3

6

9

12

15 2010

2011

r

2

 = 0.11

p-value = 0.04

Figure 25. Linear regressions of mean weekly CPUE of unmarked juvenile Fall-run Chinook 

salmon captured in Kodiak trawls (KDTRs) at the Mossdale Trawl Site and mean weekly San 

Joaquin discharge at Vernalis from November-July during the 2010 and 2011 field seasons. 
44 1.8 2.0 2.2 2.4 2.6 2.8 3.0 3.2

0

600

1200

1800

2400

3000 2010

2011

a) Winter-run

r

2

 = 0.14

p-value = 0.06

1.8 2.0 2.2 2.4 2.6 2.8 3.0 3.2

0

6000

12000

18000

24000

30000 b) Fall-run

r

2

 = 0.17

p-value = 0.01

1.8 2.0 2.2 2.4 2.6 2.8 3.0 3.2

CPUE (fish/10,000 m

3

)

0

600

1200

1800

2400

3000 c) Spring-run

r

2

 = 0.30

p-value = <0.01

Log10(Mean Discharge (m3/sec))

1.8 2.0 2.2 2.4 2.6 2.8 3.0

0

30

60

90

120

150 d) Late fall-run

r

2

 = 0.14

p-value = 0.10

Figure 26. Linear regressions of mean weekly CPUE of unmarked juvenile a) winter-, b) fall-, c) 

spring-, and d) late fall-run Chinook salmon captured in beach seines in the Lower Sacramento 

Seine Region (Region 1) and mean weekly Sacramento River discharge at Colusa from a) 

October-March, b) December-June, c) December-April, and d) August-December during the 

2010 and 2011 field seasons. 
45 2.2 2.4 2.6 2.8 3.0 3.2 3.4 3.6

0

75

150

225

300

2010

2011

a) Winter-run

r

2

 = 0.12

p-value = 0.10

2.2 2.4 2.6 2.8 3.0 3.2 3.4 3.6

CPUE (fish/10,000 m

3

)

0

4000

8000

12000

16000 b) Fall-run

r

2

 = 0.36

p-value < 0.01

2.2 2.4 2.6 2.8 3.0 3.2 3.4 3.6

0

600

1200

1800

2400

3000 c) Spring-run

r

2

 = 0.41

p-value < 0.01

Log10(Mean Discharge (m3/sec))

2.2 2.4 2.6 2.8 3.0 3.2 3.4

0

20

40

60

80 d) Late fall-run

r

2

 = 0.11

p-value = 0.21

Figure 27. Linear regressions of mean weekly CPUE of unmarked juvenile a) winter-, b) fall-, c) 

spring-, and d) late fall-run Chinook salmon captured in beach seines in the North Delta Seine

Region (Region 2) and concurrent mean weekly Sacramento River discharge at Freeport from a) 

October-March, b) December-June, c) December-April, and d) August-December during the 

2010 and 2011 field seasons. 
46

Fork Length Distributions

Unmarked juvenile Chinook salmon varied considerably in size between seine regions and trawl 

sites during the 2010 and 2011 field seasons (Figures 28-32). However, there were only weak

inter-annual differences in FLs within beach seine regions and trawl sites between the 2010 and 

2011 field seasons. In general, the FLs of unmarked juvenile Chinook salmon captured by beach 

seines during both the 2010 and 2011 field seasons displayed bimodal distributions ranging from

30-65 mm and 65-100 mm (Figures 30-32). The majority of fishes were identified as fry (FL<70

mm; Kjelson et al. 1982) and individuals were slightly (1-6 mm) smaller during the 2011 field 

season particularly within the Lower Sacramento, North Delta, and Central Delta Seine regions. 

These results are consistent with previous DJFMP findings that noted higher proportions of 

smaller individuals (i.e., fry) are observed in wet water years relative to normal or dry water 

years (Kjelson et al. 1982; Brandes and McLain 2001). In trawls, the FL distribution of 

unmarked juvenile Chinook salmon captured during both the 2010 and 2011 field seasons ranged 

from 70-110 mm using the MWTR at the Chipps Island Trawl Site (Figure 28). At the Mossdale 

Trawl Site, the FL of fish captured by the KDTR ranged from 70-120 mm (Figure 28). Fish 

captured by the KDTR and MWTR at the Sacramento Trawl Site ranged from 30-65 mm and 60-

100 mm (FL), respectively (Figure 29). In contrast to beach seine catches, the majority of fishes 

captured by trawls were identified as smolts (FL≥70 mm; Kjelson et al. 1982). However, fishes 

captured within the KDTR at the Sacramento Trawl Site were generally identified as fry. Our 

results indicate that fry and smolt sized individuals occupy both open water mid-channel and 

near shore littoral habitats. 

Although our data and other investigations (e.g., Kjelson et al. 1982) imply that fry may prefer 

near-shore littoral habitat and that smolts may prefer to occupy open water mid-channel habitat 

during the day, these patterns could be confounded by the influence of sample bias from variable 

gear efficiencies (Bayley and Peterson 2001). For example, each trawl site was sampled using 

varying trawl methods (i.e., Chipps Island = MWTR, Mossdale = KDTR, and Sacramento = 

KDTR & MWTR), cod-end designs (i.e., Mossdale = live box, Chipps Island = mesh, and 

Sacramento = mesh and live box), and cod-end "mesh" sizes (i.e., Chipps Island MWTR = 0.8

mm, Mossdale and Sacramento KDTR = 0.46 mm, and Sacramento MWTR = 0.3 mm), which 

can greatly affect the gear efficiency for different size classes of fish. Furthermore, the beach 

seine methods used by the DJFMP are thought to select for smaller individuals based on the fact 

that larger individuals are more likely able to avoid the gear during sampling. Thus the DJFMP is 

strongly considering the following changes to its standard operating procedures: (1) standardize

trawl equipment and methods among all trawl sites, (2) determine if and how gear efficiency 

varies among gear types, methods, and locations, and (3) possibly adjust catch data to better 

elucidate size and growth patterns within and among field seasons.
47

a) Chipps Island Trawl Site

n = 3,271 fish

2010

30 60 90 120 150 180

0

100

200

300

b) Chipps Island Trawl Site

n = 4,250 fish

2011

30 60 90 120 150 180

Catch Count

0

100

200

300

400

c) Mossdale Trawl Site

n = 296 fish

2010

30 60 90 120 150 180

0

4

8

12

16

20

d) Mossdale Trawl Site

n = 3,235 fish

2011

Fork Lengths (mm)

30 60 90 120 150 180

0

100

200

300

400

Figure 28. Fork length distributions of all unmarked juvenile Chinook salmon captured in midwater (MWTRs) and Kodiak trawls (KDTRs) at the Chipps Island and Mossdale Trawl sites, 

respectively during the 2010 and 2011 field seasons.
48

a) Sacramento Trawl Site

MWTR

n = 611 fish

2010

40 60 80 100 120 140

0

20

40

60

80

b) Sacramento Trawl Site

MWTR

n = 1,556 fish

2011

40 60 80 100 120 140

Catch Count

0

40

80

120

160

c) Sacramento Trawl Site

KDTR

n = 289 fish

2010

40 60 80 100 120 140

0

10

20

30

40

d) Sacramento Trawl Site

KDTR

n = 550 fish

2011

Fork Lengths (mm)

40 60 80 100 120 140

0

20

40

60

80

Figure 29. Fork length distributions of unmarked juvenile Chinook salmon captured in mid-water 

(MWTRs) and Kodiak trawls (KDTRs) at the Sacramento Trawl Site by gear during the 2010 

and 2011 field seasons.
49

a) Region 1

n = 1,089 fish

2010

40 60 80 100 120 140 160

0

20

40

60

80

c) Region 2

n = 2,556 fish

2010

40 60 80 100 120 140 160

Catch Count

0

50

100

150

200

b) Region 1

n = 3,970 fish

2011

40 60 80 100 120 140 160

0

100

200

300

400

d) Region 2

n = 4,056 fish

2011

Fork Lengths (mm)

40 60 80 100 120 140 160

0

100

200

300

Figure 30. Fork length distributions of all unmarked juvenile Chinook salmon captured in beach 

seines at the Lower Sacramento River Seine (Region 1) and North Delta Seine regions (Region 

2) during the 2010 and 2011 field seasons.
50 b) Region 3

n = 510 fish

2011

40 60 80 100 120 140 160

Catch Count

0

10

20

30

40

d) Region 4

n = 18 fish

2011

Fork Lengths (mm)

40 60 80 100 120 140 160

0.00

0.75

1.50

2.25

3.00

c) Region 4

n = 41 fish

2010

40 60 80 100 120 140 160

0

1

2

3

4

5

a) Region 3

n = 342 fish

2010

40 60 80 100 120 140 160

0

10

20

30

40

Figure 31. Fork length distributions of all unmarked juvenile Chinook salmon captured in beach 

seines at the Central Delta Seine (Region 3) and South Delta Seine regions (Region 4) during the 

2010 and 2011 field seasons.
51

a) Region 5

n = 21 fish

2011

20 40 60 80 100 120 140 160

0

1

2

3

4

b) Region 6

n = 1 fish

2010

20 40 60 80 100 120 140 160

Catch Count

0.0

0.5

1.0

1.5

2.0

c) Region 6

n = 5 fish

2011

Fork Lengths (mm)

20 40 60 80 100 120 140 160

0.0

0.5

1.0

1.5

2.0

Figure 32. Fork length distributions of all unmarked juvenile Chinook salmon captured in beach 

seines at the Lower San Joaquin River Seine (Region 5) and San Francisco/San Pablo Bay Seine 

regions (Region 6) during the 2010 and 2011 field seasons. No juvenile Chinook salmon were 

captured in Region 5 during the 2010 field season.

Absolute Abundance

Among the 74 release groups used to estimate the 

TRR

at the Chipps Island Trawl Site, a total of 

6,464,717 fish were marked with a CWT (PSMFC 2012). Release groups ranged in size from

22,911 to 717,966 individuals. The 

TRR

was estimated at 0.6% (±0.1%) after CWT releases from 

1989 to 2011. The duration of recoveries of CWT fish within a release group spanned, on 

average, 14 days. Only one release group had no recoveries. 

The mean absolute abundance of unmarked juvenile Chinook salmon emigrating out of the 

Sacramento-San Joaquin Delta was estimated at 8,995,853 and 11,562,683 individuals during the 

2010 and 2011 field seasons, respectively (Figure 33). During the 2010 field season, 

approximately 2% (n = 177,078) of the Chinook salmon were winter-run, 75% (n = 6,740,952) 

were fall-run, 23% (n = 2,046,131) were spring-run, and <1% (n = 31,691) were late fall-run

individuals. During the 2011 field season, approximately 1% (n = 166,451) of the Chinook 

salmon were winter-run, 85% (n = 9,792,957) were fall-run, 14% (n = 1,565,705) were spring-
52

run, and <1% (n = 37,569) were late fall-run individuals. In general, the absolute abundance of 

unmarked juvenile Chinook salmon at the Chipps Island Trawl Site appears to have declined 

since at least the 1990s, reaching record lows for all races during either the 2008 or 2009 field 

season (Figures 33 and 34). The abundance of unmarked juvenile winter- and late fall-run

Chinook salmon have remained at historically low levels since the 2008 field season (Figure 33). 

The abundance of both unmarked juvenile fall- and spring-run Chinook salmon at the Chipps 

Island Trawl Site have generally increased since their record low in 2008, but remain less than 

their historical averages (i.e., 1995-2009; fall = 11,236,411 and spring = 2,768,873). As reported 

by Azat (2012), the adult Chinook salmon escapement estimate for 2011 was the highest since 

2006 within the Central Valley and the fall- and spring-run portion of adult escapement 

comprised 96% of the total estimate. As a result, the increase in relative and absolute abundances 

of fall- and spring-run Chinook salmon observed during the 2010 and 2011 field seasons is likely 

attributed, in part, to a strong escapement of fall- and spring-run adults.

Contrary to previous DJFMP annual reports, we demonstrated weak linear correlation between

the historical annual absolute abundance estimates for unmarked juvenile Chinook salmon 

migrating past the Chipps Island Trawl Site and the annual adult escapement estimates for the 

Sacramento-San Joaquin River Basin (r2= 0.02; Table A26). Conversely, we found relatively 

good fit between the annual abundance estimates of juveniles at Chipps Island and adult 

escapement assuming a quadratic relationship (r2= 0.43; Figure 35). Because nearly all 

individuals captured at the Chipps Island Trawl Site are smolt sized individuals (FL≥70 mm; 

Figure 28), there is evidence that higher proportions of juvenile Chinook salmon emigrating out 

of the Delta are likely fry during years when total adult escapement exceeds 500,000, suggesting 

a possible density-dependent growth relationship within the Estuary and its watershed (Grant and 

Imre 2005). Although Brandes and McLain (2001) determined that a larger proportion of 

individuals entering and migrating through the Delta were fry during periods of high river 

discharge, there was no assessment of the influence of spawning stock or how it may interact 

with river discharge on the proportion of smolts or fry emigrating from the Delta. Further 

investigations are needed to substantiate these hypotheses.

The absolute abundance estimates for unmarked juvenile Chinook salmon migrating past Chipps 

Island presented in this report likely contains bias from several sources. Firstly, we assumed that 

unmarked individuals were never recaptured. This assumption was evidently violated based on 

the capture of CWT individuals that were released downstream of Chipps Island (e.g., San Pablo 

Bay) by the Chipps Island MWTR (Tables A24 and A25). Therefore our abundance estimates 

are overestimated to an unknown degree. Secondly, we assumed that juvenile Chinook salmon 

were equally distributed in time, which is likely violated based on diel migratory patterns. 

Several studies have demonstrated that more juvenile Chinook salmon migrate during the night 

relative to the day (Williams 2006 and references therein). As a result, given that the DJFMP 

samples during the day, the absolute abundance of unmarked juvenile Chinook salmon could be 

underestimated at Chipps Island. Thirdly, we may have underestimated the absolute abundance 

of juvenile Chinook salmon at the Chipps Island Trawl Site due to the MWTR's possible 

selectivity of smolt sized individuals, as discussed above, which could greatly bias estimates 

during wet water years (Brandes and McLain 2001). Lastly, the misidentification of race using 

the size at date of capture river criteria could greatly bias high and low race specific estimates, 

particularly for fall- and spring-run Chinook salmon (Williams 2006). 
53

Figure 33. Mean annual absolute abundance estimates and their 95% 

confidence intervals for a) winter-, b) fall-, c) spring-, and d) late fall-run 

juvenile Chinook salmon at the Chipps Island Trawl Site from the 1995 

to 2011 field seasons. Constant fractional marking (25%) of fall-run 

Chinook salmon was implemented by hatcheries in 2007 (tagging rates 

varied prior to 2007).

0

200,000

400,000

600,000

800,000

1,000,000

1,200,000

1995 1997 1999 2001 2003 2005 2007 2009 2011

a) Winter-run

0

5,000,000

10,000,000

15,000,000

20,000,000

25,000,000

30,000,000

1995 1997 1999 2001 2003 2005 2007 2009 2011

b) Fall-run

0

1,500,000

3,000,000

4,500,000

6,000,000

7,500,000

9,000,000

1995 1997 1999 2001 2003 2005 2007 2009 2011

c) Spring-run

0

50,000

100,000

150,000

200,000

250,000

300,000

350,000

1995 1997 1999 2001 2003 2005 2007 2009 2011

d) Late fall-run

Absolute Abundance
54

Figure 34. Mean absolute abundance estimates and their 95% confidence 

intervals for fall-run juvenile Chinook salmon at the Chipps Island Trawl Site 

during April through June from the 1978 to 2011 field seasons. Constant 

fractional marking (25%) of fall-run Chinook was implemented by hatcheries 

in 2007 (tagging rates varied prior to 2007).

Figure 35. Mean annual absolute abundance estimates for all unmarked juvenile 

Chinook salmon at the Chipps Island Trawl Site related to total adult Chinook salmon 

escapement for the Sacramento-San Joaquin River Basin from 1995 to 2011.

0

5,000,000

10,000,000

15,000,000

20,000,000

25,000,000

30,000,000

35,000,000

40,000,000

45,000,000

1978 1981 1984 1987 1990 1993 1996 1999 2002 2005 2008 2011

Absolute Abundance

y = -8E-05x2 + 78.652x - 869892

R2 = 0.4264

0

5,000,000

10,000,000

15,000,000

20,000,000

25,000,000

30,000,000

35,000,000

0 200,000 400,000 600,000 800,000 1,000,000

Absolute Abundance 

Adult Escapement
55

Steelhead

We captured 188 and 154 steelhead during the 2010 and 2011 field seasons, respectively (Tables 

A18 and A19). Approximately 90% of all steelhead captured in 2010 (n = 171) and 2011 (n = 

140) were marked and considered to be hatchery reared. 

Distribution and Relative Abundance

The DJFMP captured steelhead in low numbers at all trawl sites during the 2010 and 2011 field 

seasons with the majority of observations at Chipps Island (Tables A18 and A19). Both 

hatchery-reared and wild steelhead were generally detected from January through May at the 

Chipps Island Trawl Site and January through June at the Sacramento Trawl Site (Figures 36 and 

37). The mean monthly CPUE at the Chipps Island and Sacramento Trawl sites peaked in 

February. Relatively few individuals (total<5 per field season) were detected at the Mossdale

Trawl Site primarily during April and May (Figure 38). Although the 2010 and 2011 mean 

yearly CPUE estimates at the Chipps Island Trawl Site were similar to those observed over the 

last decade, the total number of wild individuals have steadily declined since 1995 and were near 

record lows during the 2010 and 2011 field seasons (Figure 36). Because all hatchery reared 

steelhead within the Central Valley have been marked for management purposes since 1998 

(Kevin Niemela, USFWS, personal communication), the decline in wild steelhead CPUE from 

1998 through 2011 can be a result of declining wild stock(s). Lower CPUE estimates for wild 

fish are consistent with natural escapement estimates (McEwan 2001). No trends of mean yearly 

CPUE estimates at the Sacramento and Mossdale Trawl sites were apparent (Figures 37 and 38).

In beach seines, steelhead were generally detected in very low numbers and only within the 

Lower Sacramento River, North Delta, and Central Delta Seine regions (Figures 39 and 40). 

Steelhead were observed from January through February and January through March during the 

2010 and 2011 field seasons, respectively. Only one wild steelhead was detected in 2010 and this 

individual was observed in the Lower Sacramento River Seine Region. All wild steelhead 

observed in 2011 (n=3) were detected in the North Delta Seine Region. The trends of mean 

yearly CPUE estimates for wild and hatchery reared steelhead within seine regions were

inconclusive based on consistently low catch numbers (Figures 39 and 40).

Influence of River Discharge

During the 2010 and 2011 field seasons, the mean monthly CPUE of all steelhead generally 

peaked during the same months at each trawl site or seine region regardless of mean monthly 

river discharge (e.g., during February at Chipps Island; Figure 36). In addition, there was

generally no discernible difference between the mean monthly CPUE estimates at any given 

location between years, suggesting there was little influence of water year type on the relative 

abundance of steelhead. Previous investigations have indicated that wild and hatchery reared

juvenile steelhead migrate at higher rates during periods of higher river discharges (Giorgi et al. 

1997). However, because the majority of individuals that the DJFMP captured were hatchery 

reared, steelhead catches were likely highly influenced by the timing and location of hatchery 

releases and less likely influenced by river discharge. Many of the hatchery reared steelhead 

were captured in beach seines that are at or near known hatchery release sites. Therefore, the 
56

capture of primarily hatchery-reared steelhead combined with relatively low catches of wild 

steelhead likely created relatively poor relationships between river discharge and steelhead 

densities.

Fork Length Distributions

Due to low captures of steelhead, trends were weak or not apparent for the 2010 and 2011 

length-frequency distributions (Figures 41-46). The FL of steelhead captured by the DJFMP 

generally ranged from 200 to 300 mm among the trawl sites and 160 to 300 mm among seine 

regions. Steelhead captured by the DJFMP did not appear to vary in size among gear types, seine 

regions, or trawl sites. However, the FL of wild steelhead was slightly smaller (more individuals 

with FL<120 mm) relative to hatchery reared steelhead at the Sacramento and Mossdale Trawl 

sites and North Delta Seine Region (Figures 42-46). Again, this trend is likely a result of the 

small sample size. 

If we assume that size-specific sampling efficiency is similar for steelhead and Chinook salmon 

and seines and KDTR gears are effective at sampling small fish (FL<70 mm), our results indicate 

that juvenile steelhead entering and migrating through the Sacramento-San Joaquin Delta are 

mostly large individuals from multiple age classes. Lindley et al. (2006) showed that the lower 

San Joaquin River and the Sacramento-San Joaquin Delta were mostly unsuitable for rearing 

based on relatively high water temperatures, making the Delta function primarily as a migratory 

corridor. Furthermore, it was determined that wild juvenile steelhead from the Sacramento River 

Basin spend one to three years (average = two) rearing in fresh water before emigrating 

(Williams 2006 and references therein), suggesting that smaller juvenile steelhead from the 

Sacramento River are not using the Delta for rearing habitat. Lastly, in an attempt to maximize 

survival, fish hatcheries often rear steelhead to larger sizes before releasing them within or just 

upstream of the Estuary. Although the DJFMP is able to detect small numbers of larger juvenile 

steelhead during each field season, we presume that DJFMP methods are not very efficient in 

catching these large and highly mobile individuals. Therefore, the DJFMP may not be adequately 

monitoring juvenile steelhead within the San Francisco Estuary and sampling efficiency needs to 

be determined. An investigation of sampling efficiency would help elucidate this uncertainty. 
57

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

0.0

0.1

0.2

0.3

0.4

0

200

400

600

800

1000

2010_Chipps_Month_RBT 

2010_Chipps_Month_RBTc 

Plot 5 Zero

a) Steelhead

2010

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

CPUE (fish/10,000 m

3

)

0.00

0.03

0.06

0.09

0.12

0.15

0.18

Mean Discharge (m

3/sec)

0

1000

2000

3000

4000

wild, n = 8 fish

hatchery, n = 92 fish

1995 1997 1999 2001 2003 2005 2007 2009 2011

0.00

0.02

0.04

0.06

0.08

0.10

0.12

0

400

800

1200

1600

2000

b) Steelhead

2011

c) Steelhead

Inter-Annual

wild, n = 6 fish

hatchery, n = 113 fish

Figure 36. Mean monthly and yearly CPUE (bars) of hatchery and wild steelhead captured in 

mid-water trawls (MWTRs) at the Chipps Island Trawl Site, and mean monthly and yearly Delta 

discharge (lines) during the a) 2010, b) 2011, and c) 1995 through 2011 field seasons. Sample 

size (n) corresponds to total number of fish caught.
58

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

0.00

0.05

0.10

0.15

0.20

0.25

0.30

0

200

400

600

800

1000 a) Steelhead

2010

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

CPUE (fish/10,000 m

3

)

0.00

0.05

0.10

0.15

0.20

0.25

0.30

0.35

Mean Discharge (m

3/sec)

0

400

800

1200

1600

2000

2001 2003 2005 2007 2009 2011

0.00

0.05

0.10

0.15

0.20

0.25

0.30

0.35

0

300

600

900

1200

MWTR, wild, n = 2

MWTR, hatchery, n = 1

KDTR, wild, n = 0

KDTR, hatchery, n = 37

b) Steelhead

2011

c) Steelhead

Inter-Annual

MWTR, wild, n = 3

MWTR, hatchery, n = 4

KDTR, wild, n = 4

KDTR, hatchery, n = 29

Figure 37. Mean monthly and yearly CPUE (bars) of hatchery and wild steelhead captured in 

mid-water (MWTRs) and Kodiak trawls (KDTRs) at the Sacramento Trawl Site, and mean 

monthly and yearly Sacramento River discharge at Freeport (lines) during the a) 2010, b) 2011, 

and c) 2000 through 2011 field seasons. Sample size (n) corresponds to total number of fish 

caught.
59

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

0.000

0.003

0.006

0.009

0.012

0.015

0

30

60

90

120

150 a) Steelhead

2010

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

CPUE (fish/10,000 m

3

)

0.000

0.002

0.004

0.006

0.008

0.010

Mean Discharge (m

3/sec)

0

200

400

600

800

2004 2005 2006 2007 2008 2009 2010 2011

0.000

0.003

0.006

0.009

0.012

0.015

0

75

150

225

300

wild, n = 3

hatchery, n = 0

b) Steelhead

2011

c) Steelhead

Inter-Annual

wild, n = 3

hatchery, n = 1

Figure 38. Mean monthly and yearly CPUE (bars) of hatchery and wild steelhead captured in 

Kodiak trawls (KDTRs) at the Mossdale Trawl Site, and mean monthly and yearly San Joaquin 

River discharge at Vernalis (lines) during the a) 2010, b) 2011, and c) 2004 through 2011 field 

seasons. Sample size (n) corresponds to total number of fish caught.
60

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

0

2

4

6

8

0

200

400

600

800

1000 a) Steelhead (wild)

n = 1

2010

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

CPUE (fish/10,000 m

3

)

0

2

4

6

8

10

12

Mean Discharge (m

3/sec)

0

600

1200

1800

2400

3000

3600

2001 2003 2005 2007 2009 2011

0

2

4

6

8

10

0

300

600

900

1200

1500

1800

Region 1

Region 2

Region 3

Region 6

Delta Outflow

Vernalis

Freeport

b) Steelhead (wild)

n = 3

2011

c) Steelhead (wild)

Inter-Annual

Figure 39. Mean monthly and yearly CPUE of wild steelhead captured in beach seines at 

Regions 1-6, and mean monthly and yearly Sacramento River discharge at Freeport, San Joaquin 

River discharge at Vernalis, and Delta discharge during the a) 2010, b) 2011, and c) 2000 

through 2011 field seasons. Sample size (n) corresponds to total number of fish caught.
61

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

0

20

40

60

80

100

120

0

200

400

600

800

1000 a) Steelhead (hatchery)

n = 25

2010

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

CPUE (fish/10,000 m

3

)

0

10

20

30

40

50

Mean Discharge (m

3/sec)

0

600

1200

1800

2400

3000

3600

2001 2003 2005 2007 2009 2011

0

5

10

15

20

25

30

0

300

600

900

1200

1500

1800

b) Steelhead (hatchery)

n = 9

2011

c) Steelhead (hatchery)

Inter-Annual

Region 1

Region 2

Region 3

Region 5

Delta Outflow

Vernalis

Freeport

Figure 40. Mean monthly and yearly CPUE of hatchery steelhead captured in beach seines at 

Regions 1-6, and mean monthly and yearly Sacramento River discharge at Freeport, San Joaquin 

River discharge at Vernalis, and Delta discharge during the a) 2010, b) 2011, and c) 2000 

through 2011 field seasons. Sample size (n) corresponds to total number of fish caught.
62

a) Chipps Island Trawl Site

Steelhead (wild)

n = 6 fish

2010

100 150 200 250 300 350 400

0

1

2

b) Chipps Island Trawl Site

Steelhead (wild)

n = 8 fish

2011

100 150 200 250 300 350 400

0

1

2

3

c) Chipps Island Trawl Site

Steelhead (hatchery)

n = 113 fish

2010

100 150 200 250 300 350 400

Catch Count

0

2

4

6

d) Chipps Island Trawl Site

Steelhead (hatchery)

n = 92 fish

2011

Fork Lengths (mm)

100 150 200 250 300 350 400

0

2

4

6

Figure 41. Fork length distributions for all hatchery and wild steelhead captured in mid-water 

trawls (MWTRs) at the Chipps Island Trawl Site during the 2010 and 2011 field seasons.
63

a) Sacramento Trawl Site

MWTR

Steelhead (wild)

n = 3 fish

2010

60 120 180 240 300

0

1

2

3

b) Sacramento Trawl Site

MWTR

Steelhead (wild)

n = 2 fish

2011

60 120 180 240 300

Catch Count

0

1

2

3

c) Sacramento Trawl Site

KDTR

Steelhead (wild)

n = 4 fish

2010

Fork Lengths (mm)

60 120 180 240 300

0

1

2

3

Figure 42. Fork length distributions for wild steelhead captured in mid-water (MWTRs) and 

Kodiak trawls (KDTRs) at the Sacramento Trawl Site during the 2010 and 2011 field seasons.

No wild steelhead were captured at the Sacramento Trawl Site during the 2011 field season using 

KDTRs.
64

a) Sacramento Trawl Site

MWTR

Steelhead (hatchery)

n = 4 fish

2010

100 200 300 400 500

0

1

2

3

b) Sacramento Trawl Site

MWTR

Steelhead (hatchery)

n = 1 fish 

2011

100 200 300 400 500

0

1

2

3

c) Sacramento Trawl Site

KDTR

Steelhead (hatchery)

n = 29 fish

2010

100 200 300 400 500

Catch Count

0

1

2

3

4

d) Sacramento Trawl Site

KDTR

Steelhead (hatchery)

n = 37 fish

2011

Fork Lengths (mm)

100 200 300 400 500

0

1

2

3

4

Figure 43. Fork length distributions for hatchery steelhead captured in mid-water (MWTRs) and 

Kodiak trawls (KDTRs) at the Sacramento Trawl Site during the 2010 and 2011 field seasons.
65

a) Mossdale Trawl Site

Steelhead (wild)

n = 3 fish

2010

180 210 240 270 300 330 360

0

1

2

3

b) Mossdale Trawl Site

Steelhead (wild)

n = 3 fish

2011

180 210 240 270 300 330 360

Catch Count

0

1

2

3

c) Mossdale Trawl Site

Steelhead (hatchery)

n = 1 fish

2011

Fork Lengths (mm)

180 210 240 270 300 330 360

0

1

2

3

Figure 44. Fork length distributions for hatchery and wild steelhead captured in Kodiak trawls

(KDTRs) at the Mossdale Trawl Site during the 2010 and 2011 field seasons. No hatchery 

steelhead were captured at the Mossdale Trawl Site during the 2010 field season.
66

a) Region 1

Steelhead (wild)

n = 1 fish

2010

80 120 160 200 240 280

0

1

2

3

b) Region 1

Steelhead (hatchery)

n = 9 fish

2010

80 120 160 200 240 280

0

1

2

3

c) Region 2

Steelhead (hatchery)

n = 14 fish

2010

80 120 160 200 240 280

Catch Count

0

1

2

3

d) Region 3

Steelhead (hatchery)

n = 2 fish

2010

Fork Lengths (mm)

80 120 160 200 240 280

0

1

2

3

Figure 45. Fork length distributions for hatchery and wild steelhead captured in beach seines

within the Lower Sacramento River (Region 1), North Delta (Region 2), and Central Delta 

(Region 3) Seine regions during the 2010 field season.
67

a) Region 1

Steelhead (hatchery)

n = 7 fish

2011

80 120 160 200 240 280

0.0

1.5

3.0

4.5

b) Region 2

Steelhead (wild)

n = 3 fish

2011

80 120 160 200 240 280

0

1

2

3

c) Region 2

Steelhead (hatchery)

n = 1 fish

2011

80 120 160 200 240 280

Catch Count

0

1

2

3

d) Region 3

Steelhead (hatchery)

n = 1 fish

2011

Fork Lengths (mm)

80 120 160 200 240 280

0.0

0.5

1.0

1.5

2.0

Figure 46. Fork length distributions for hatchery and wild steelhead captured in beach seines 

within the Lower Sacramento River (Region 1), North Delta (Region 2), and Central Delta 

(Region 3) Seine regions during the 2011 field season.
68

Delta Smelt

A total of 390 and 373 delta smelt were captured by the DJFMP during the 2010 and 2011 field 

seasons, respectively (Tables A18 and A19). 

Distribution and Relative Abundance

The majority (>75%) of delta smelt were captured at the Chipps Island Trawl Site during the 

2010 and 2011 field seasons (Tables A18 and A19). Although delta smelt were captured in most 

months, the mean monthly CPUE at Chipps Island peaked in summer (July and August) and 

autumn (November) and was lowest in spring (April and May) in 2010. Similarly, CPUE peaked 

in August and December and was lowest in spring (April and May) in 2011 (Figure 47). In 2010, 

we captured one delta smelt at the Sacramento and Mossdale Trawl sites during March and June, 

respectively (Figures 48 and 49). No delta smelt were captured at the Sacramento and Mossdale 

Trawl sites during the 2011 field season. The mean yearly CPUE estimates suggest that delta 

smelt at the Chipps Island and Sacramento Trawl sites were near record lows during both years. 

The mean yearly CPUE estimates at the Mossdale Trawl Site were also low and similar to those 

observed since 2004. The declines of mean yearly CPUE at all trawl sites is likely a result of a 

precipitous drop in population size starting in the early 2000s (Sommer et al. 2007; Contreras et 

al. 2012).

Delta smelt were primarily captured using beach seines within the North Delta Seine Region 

from December to April during the 2010 field season (Figure 50). We captured one and two 

individuals within the South Delta and Central Delta Seine regions, respectively. During the 

2011 field season, delta smelt were detected only within the North Delta Seine Region generally 

from February to August. Peak monthly CPUE occurred in February and March during the 2010 

and 2011 field seasons, respectively. The mean yearly CPUE estimates suggest that delta smelt 

were observed in higher densities consistently within the North Delta Seine Region relative to 

other seine regions since the 2000 field season, and that the densities within the North Delta have 

increased annually since the record low was observed in 2008 (Figure 50).

Delta smelt are generally confined to the upper portions of the San Francisco Estuary (i.e., 

Suisun Bay and Delta) based on their life history strategy (Moyle et al. 1992). Delta smelt 

typically have a one year life cycle and reside primarily in and near the low salinity zone (1-6

ppt) except when they migrate into freshwater and spawn during the spring (Stevens et al. 1990, 

Moyle et al. 1992; Jassby et al. 1995; Dege and Brown 2004). The relatively high monthly 

CPUEs observed during the winter and summer at the Chipps Island Trawl Site throughout the 

2010 and 2011 field seasons is likely a result of juveniles and sub-adults residing within or 

migrating through Suisun Bay (near the low salinity zone) during the summer and adults later 

migrating upstream into the Delta during the spring to reproduce. The occurrence of delta smelt 

in the Mossdale and Sacramento Trawl sites and within the interior Delta seine regions during 

the spring is likely an indication of immigration, spawning, rearing, and/or emigration within the 

freshwater Delta. Although our catch data appears to broadly illustrate shifts in distribution and 

changes in population size during particular life stages, more robust IEP surveys are conducted 

to monitor the distribution and relative abundance of delta smelt within the Estuary. 
69

Influence of River Discharge

Mean monthly and yearly CPUE of delta smelt at the Chipps Island Trawl Site showed little to 

no relationship to river discharge during the 2010 and 2011 field seasons (Figure 47). This may 

be due to the Chipps Island MWTR primarily capturing delta smelt as they migrate to and from 

the low salinity zone further downstream. Although the mean monthly CPUE of delta smelt 

appeared correlated with mean monthly river discharge within the North Delta Seine Region, we 

failed to detect a relationship between mean weekly CPUE and mean weekly river discharges 

during December through April in 2010 and from February through July in 2011 (n = 46, r

2

= 

0.028, p-value = 0.75). Overall, our results suggest that river discharge does not appear to 

directly influence DJFMP catch densities. This finding is supported by the conclusions of more 

thorough investigations (e.g., Stevens and Miller 1983; Dege and Brown 2004; Miller et al. 

2012). Stevens and Miller (1983) found no significant correlation between delta smelt abundance 

indices during the fall and Delta inflow during the spring and summer. Similarly, Dege and 

Brown (2004) demonstrated that there was no significant relationship between the abundance 

indices of larval or juvenile delta smelt and Delta outflow. Therefore the effect of river discharge 

on DJFMP delta smelt catch densities appears to be indirect through influencing the position of 

the low salinity zone which affects the distribution of delta smelt (Dege and Brown 2004).

Fork Length Distributions

The length-frequency distribution of delta smelt captured at the Chipps Island Trawl Site during

the 2010 and 2011 field seasons generally ranged from 45 to 95 mm (FL), with most individuals

measuring between 60 and 70 mm (Figure 51). The FLs observed at the Mossdale and 

Sacramento Trawl sites during the 2010 field season were 25 mm and 70 mm, respectively. The 

FLs within beach seine regions generally ranged from 59 to 77 mm in 2010 and from 26 to 87 

mm in 2011 (Figures 52 and 53). Although the 25mm (FL) delta smelt captured at the Mossdale 

Trawl Site during June 2010 seems unlikely, this fish was identified by the DFG within their 

Region 4 laboratory. These data suggest that the DJFMP captured either sub-adults or adults 

migrating into and from Suisun Bay and either juveniles or adults migrating to and from the 

Delta pre and post spawn during the 2010 and 2011 field seasons.
70

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

0.00

0.05

0.10

0.15

0.20

0.25

0

200

400

600

800

1000 a) Delta smelt

n = 294

2010

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

CPUE (fish/10,000 m

3

)

0.0

0.1

0.2

0.3

0.4

0.5

Mean Discharge (m

3/sec)

0

1000

2000

3000

4000

2001 2003 2005 2007 2009 2011

0

1

2

3

4

5

0

400

800

1200

1600

2000

b) Delta smelt

n = 315

2011

c) Delta smelt

Inter-Annual

Figure 47. Mean monthly and yearly CPUE of delta smelt captured in mid-water trawls 

(MWTRs) at the Chipps Island Trawl Site, and mean monthly and yearly Delta discharge during 

the a) 2010, b) 2011, and c) 2000 through 2011 field seasons. Sample size (n) corresponds to 

total number of fish caught.
71

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

0.000

0.003

0.006

0.009

0.012

0

200

400

600

800

1000 a) Delta smelt

2010

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

CPUE (fish/10,000 m

3

)

0.0

0.2

0.4

0.6

0.8

1.0

Mean Discharge (m

3/sec)

0

400

800

1200

1600

2000

2001 2003 2005 2007 2009 2011

0.0000

0.0075

0.0150

0.0225

0.0300

0.0375

0

300

600

900

1200

MWTR, n = 0

KDTR, n = 0

b) Delta smelt

2011

c) Delta smelt

Inter-Annual

MWTR, n = 0

KDTR, n = 1

Figure 48. Mean monthly and yearly CPUE of delta smelt captured in mid-water (MWTRs) and 

Kodiak trawls (KDTRs) at the Sacramento Trawl Site, and mean monthly and yearly Sacramento 

River discharge at Freeport during the a) 2010, b) 2011, and c) 2000 through 2011 field seasons. 

Sample size (n) corresponds to total number of fish caught.
72

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

0.000

0.004

0.008

0.012

0.016

0.020

0

40

80

120

a) Delta smelt 160

n = 1

2010

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

Mean Discharge (m

3/sec)

0

200

400

600

800

CPUE (fish/10,000 m

3

)

0.0

0.2

0.4

0.6

0.8

1.0

2004 2005 2006 2007 2008 2009 2010 2011

0.000

0.002

0.004

0.006

0.008

0

75

150

225

300

b) Delta smelt

n = 0

2011

c) Delta smelt

Inter-Annual

Figure 49. Mean monthly and yearly CPUE of delta smelt captured in Kodiak trawls (KDTRs) at 

the Mossdale Trawl Site, and mean monthly and yearly San Joaquin River discharge at Vernalis 

during the a) 2010, b) 2011, and c) 2004 through 2011 field seasons. Sample size (n) corresponds 

to total number of fish caught.
73

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

0

50

100

150

200

250

300

0

200

400

600

800

a) Delta smelt 1000

n = 94

2010

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

CPUE (fish/10,000 m

3

)

0

50

100

150

200

Mean Discharge (m

3/sec)

0

600

1200

1800

2400

3000

3600

2001 2003 2005 2007 2009 2011

0

10

20

30

40

50

0

300

600

900

1200

1500

1800

Region 1

Region 2

Region 3

Region 4

Region 5

Region 6

Delta Outflow

Vernalis

Freeport

b) Delta smelt

n = 58

2011

c) Delta smelt

Inter-Annual

Figure 50. Mean monthly and yearly CPUE of delta smelt captured in beach seines at Regions 1-

6, and mean monthly and yearly Sacramento River discharge at Freeport, San Joaquin River 

discharge at Vernalis, and Delta discharge during the a) 2010, b) 2011, and c) 2000 through 2011 

field seasons. Sample size (n) corresponds to total number of fish caught.
74

a) Chipps Island Trawl Site

n = 294 fish

2010

30 40 50 60 70 80 90 100

0

10

20

30

40

b) Chipps Island Trawl Site

n = 315 fish 

2011

Fork lengths (mm)

30 40 50 60 70 80 90 100

Catch Count

0

10

20

30

Figure 51. Fork length distributions for all delta smelt captured in mid-water trawls (MWTRs) at 

the Chipps Island Trawl Site during the 2010 and 2011 field seasons.

a) Region 2

n = 91 fish

2010

30 45 60 75 90

0

5

10

15

20

b) Region 3

n = 2 fish

2010

30 45 60 75 90

Catch Count

0

1

2

3

c) Region 4

n = 1 fish

2010

Fork Lengths (mm)

30 45 60 75 90

0

1

2

3

Figure 52. Fork length distributions for delta smelt captured in beach seines within the North 

Delta (Region 2), Central Delta (Region 3), and South Delta (Region 4) Seine regions during the 

2010 field season.
75 Region 2

n = 58 fish

2011

Fork Lengths (mm)

30 40 50 60 70 80 90 100

Catch Count

0

4

8

12

Figure 53. Fork length distributions for delta smelt captured in beach seines within the North 

Delta Seine Region (Region 2) during the 2011 field season.

Longfin Smelt

We captured 584 and 219 longfin smelt during the 2010 and 2011 field seasons, respectively 

(Tables A18 and A19). 

Distribution and Relative Abundance

All longfin smelt observed during the 2010 field season and nearly all longfin smelt (~98%) 

observed during the 2011 field season were detected at the Chipps Island Trawl Site (Tables A18 

and A19). No longfin smelt were captured at the Mossdale or Sacramento Trawl sites. The 

majority of longfin smelt were caught at the Chipps Island Trawl Site from December to March 

during the 2010 field season and from December to January in 2011 (Figure 54). The mean

yearly CPUE for longfin smelt at Chipps Island declined in 2003 and has remained relatively low 

through 2011 (Figure 54). As with delta smelt, the declines of longfin smelt mean yearly CPUE 

at the Chipps Island Trawl Site is likely a result of a precipitous drop in population size starting 

in the early 2000s (Sommer et al. 2007; Contreras et al. 2012).

We did not collect longfin smelt in beach seines in 2010 and only four individuals were caught 

during the 2011 field season (Tables A18 and A19). Three of the four longfin smelt observed in 

2011 were captured within the San Francisco/San Pablo Bay Seine Region during August and 

one individual was captured within the North Delta Seine Region in December (Figure 55).

Mean yearly CPUE estimates indicate that longfin smelt have only been captured within these 

seine regions at relatively low densities (Figure 55).

Longfin smelt are short lived and adults primarily reside in and near the San Francisco and San 

Pablo bays where the salinity ranges from 15-30ppt (Moyle 2002). Starting as early as November 

through June, adults migrate and spawn further upstream within the Estuary in the lower portions 

of the Delta and Upper Suisun Bay (Moyle 2002). Because the occurrence and relatively high 

monthly CPUEs observed by the DJFMP were typically isolated from December to March 

upstream of San Pablo Bay, individuals observed were likely adults migrating pre or post spawn.

However, our longfin smelt catch data reported here should be used only as anecdotal 

information for migration timing based on the limited catch data. More robust IEP surveys are 

conducted to monitor the distribution and relative abundance of longfin smelt within the Estuary.
76

Influence of River Discharge

Although previous studies have reported a positive correlation between longfin smelt abundance 

and Delta discharge (Stevens and Miller 1983; Rosenfield and Baxter 2007), mean yearly CPUE 

at the Chipps Island Trawl Site has shown a consistent decline regardless of flow since the 2003 

field season (Figure 54). However, our results suggest that the peak mean monthly CPUE of 

longfin smelt at the Chipps Island Trawl Site may be positively related to the first large increase 

in river discharge prior to or during their spawning period (i.e., November to June). In 2010, the 

mean daily Delta discharge increased from 158 to 1,897m

3

/sec over 11 consecutive days during 

late January and mean monthly CPUE peaked soon after in February. In 2011, the mean daily 

Delta discharge increased from 239 to 2,478 m

3

/sec over 20 consecutive days during the middle 

of December and mean monthly CPUE peaked during the same month. Further investigation is 

needed to substantiate this hypothesis understanding that the migration of longfin smelt is likely 

influenced by a multitude of physical variables, biological factors, and their interactions. 

Fork Length Distributions

The length-frequency distributions of longfin smelt captured at the Chipps Island Trawl Site 

generally ranged from 70 to 140 mm and from 90 to 140 mm (FL) during the 2010 and 2011 

field seasons, respectively (Figure 56). During the 2011 field season, individuals captured within 

the San Francisco/San Pablo Bay Seine Region were <44 mm (FL) and the individual captured 

within the North Delta Seine Region had a 103 mm FL (Figure 57). These data suggest that the 

majority of the longfin smelt were adults either migrating into the Delta from Suisun Bay to 

spawn or migrating into Suisun Bay from the Delta post spawn. 
77

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

0.0

0.2

0.4

0.6

0.8

1.0

0

200

400

600

800

1000 a) Longfin smelt

n = 584

2010

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

CPUE (fish/10,000 m

3

)

0.0

0.2

0.4

0.6

0.8

Mean Discharge (m

3/sec)

0

1000

2000

3000

4000

2001 2003 2005 2007 2009 2011

0

1

2

3

4

5

0

400

800

1200

1600

2000

b) Longfin smelt

n = 215

2011

c) Longfin smelt

Inter-Annual

Figure 54. Mean monthly and yearly CPUE of longfin smelt captured in mid-water trawls 

(MWTRs) at the Chipps Island Trawl Site, and mean monthly and yearly Delta discharge during 

the a) 2010, b) 2011, and c) 2000 through 2011 field seasons. Sample size (n) corresponds to 

total number of fish caught.
78

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

0

200

400

600

800

1000

0.00

0.25

0.50

0.75

1.00 a) Longfin smelt

n = 0

2010

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

Mean Discharge (m

3/sec)

0

600

1200

1800

2400

3000

3600

CPUE (fish/10,000 m

3

)

0

4

8

12

16

20

2001 2003 2005 2007 2009 2011

0.0

0.5

1.0

1.5

2.0

2.5

3.0

0

300

600

900

1200

1500

1800

Region 2

Region 6

Delta Outflow

Vernalis

Freeport

b) Longfin smelt

n = 4

2011

c) Longfin smelt

Inter-Annual

Figure 55. Mean monthly and yearly CPUE of longfin smelt captured in beach seines at Regions 

1-6, and mean monthly and yearly Sacramento River discharge at Freeport, San Joaquin River 

discharge at Vernalis, and Delta discharge during the a) 2010, b) 2011, and c) 2000 through 2011 

field seasons. Sample size (n) corresponds to total number of fish caught.
79

a) Chipps Island Trawl Site

n = 584 fish

2010

40 60 80 100 120 140 160

0

10

20

30

40

b) Chipps Island Trawl Site

n = 215 fish

2011

Fork Lengths (mm)

40 60 80 100 120 140 160

Catch Count

0

6

12

18

Figure 56. Fork length distributions for all longfin smelt captured in mid-water trawls (MWTRs) 

at the Chipps Island Trawl Site during the 2010 and 2011 field seasons.

a) Region 2

n = 1 fish

2011

30 45 60 75 90 105

Catch Count

0

1

2

3

b) Region 6

n = 3 fish

2011

Fork Lengths (mm)

30 45 60 75 90 105

0

1

2

3

Figure 57. Fork length distributions for longfin smelt captured in beach seines within the North 

Delta (Region 2) and San Francisco/San Pablo Bay (Region 6) Seine regions during the 2011 

field season.
80

Sacramento Splittail

A total of 10,023 and 115,117 Sacramento splittail were captured by the DJFMP during the 2010 

and 2011 field seasons, respectively (Tables A18 and A19). 

Distribution and Relative Abundance

Sacramento splittail were captured in nearly all seine regions and trawl sites during the 2010 and 

2011 field season (Tables A18 and A19). At the Chipps Island Trawl Site, individuals were 

generally captured throughout the 2010 field season, and during December through April and 

July in the 2011 field season (Figure 58). The mean monthly CPUE estimates peaked during 

January and July in 2010 and during December and July in 2011 (Figure 58). In contrast, we 

only captured one individual in 2010 and four individuals in 2011 at the Sacramento Trawl Site 

(Figure 59). The mean yearly CPUE at the Chipps Island and Sacramento Trawl sites were near 

record lows during the 2010 and 2011 field season. The majority of all individuals captured by 

DJFMP trawls were caught at the Mossdale Trawl Site from May to July during both field years

with peak catches in May (Figure 60). The mean yearly CPUE at the Mossdale Trawl Site was 

relatively low in 2010, but increased considerably in 2011 to become the second highest yearly 

CPUE observed since 2004 (Figure 60).

In beach seines, Sacramento splittail were captured from April through July and May through 

July during the 2010 and 2011 field seasons, respectively (Figure 61). However, no captures 

were reported at the San Francisco/San Pablo Seine Region during the 2010 field season. The 

mean monthly CPUE peaked in nearly all seine regions during May. The mean yearly CPUE 

estimates suggest that Sacramento splittail were generally observed in higher densities within the 

Lower San Joaquin River and Central Delta Seine regions relative to other seine regions since 

the 2000 field season. Densities within all seine regions increased to record highs during the 

2011 field season compared to catches from 2000 through 2010 (Figure 61).

Sacramento splittail are a relatively long lived (7-9 years), endemic to the Central Valley, and 

primarily reside within the lower portions of the San Francisco Estuary (Young and Cech 1996;

Moyle et al. 2004). In general, adults migrate upstream from as early as November to February 

and can spawn from January to April within low gradient portions of the Sacramento River, San 

Joaquin River, and tributaries (Sommer et al. 1997; Moyle et al. 2004). In addition, studies have 

demonstrated that offspring subsequently migrate downstream within the Estuary from April 

through June to rear in shallow brackish habitats (Feyrer et al. 2005). Therefore, the increase in 

the mean monthly CPUE of Sacramento splittail at the Chipps Island Trawl Site during the 

winter of both field seasons likely reflected adult spawning migrations. Whereas the increase in 

the mean monthly CPUE from May to July at most trawl sites and within all beach seine regions 

was likely a result of juveniles migrating downstream to the lower portions of the Estuary.

Influence of River Discharge

The relatively high mean yearly CPUE observed during the 2011 field season at the Mossdale 

Trawl Site and within all seine regions was likely a result of higher river discharges, extended 

floodplain inundation, and lower water temperatures, particularly within the San Joaquin River 
81

Basin (Tables A20 and A23; Figures 60 and 61). Sacramento splittail are obligate floodplain 

spawners and numerous investigations have demonstrated that year class strength is positively 

associated with wet water years and high river discharges (Sommer et al. 1997; Sommer et al. 

2001; Moyle et al. 2004). While splittail can spawn without floodplain access, they do require

fairly continuous floodplain inundation at least one month in duration to produce strong year 

classes (Sommer et al. 1997; Sommer et al. 2001; Moyle et al. 2004). Because the San Joaquin 

River is less channelized than the Sacramento River, the San Joaquin River and its tributaries 

presumably have more floodplain spawning habitat during wet water years, which likely 

contributed to the higher mean CPUEs observed near and within the Lower San Joaquin River 

from May through July. 

During the 2010 and 2011 field seasons, the mean monthly CPUE of Sacramento splittail

generally peaked at the Chipps Island Trawl Site during increased mean Delta discharge (Figure 

58) from November to January, suggesting a positive correlation during the adult upstream 

migration period (Moyle et al. 2004). To better understand the influence of Delta discharge on 

adult migration near and within Suisun Bay, we developed a simple linear regression model of 

mean weekly CPUE and log10 of the weekly mean Delta discharge data at the Chipps Island 

Trawl Site. Assuming a linear relationship, we showed a significant positive correlation (p-value 

= 0.04) where 31% of the variability in the mean weekly CPUE from November to January could 

be explained by Delta discharge (Figure 62). Our results support the hypothesis of Moyle et al. 

(2004) that intra-annual river discharge likely influences the timing and magnitude of adults 

migrating upstream prior to spawning.

In addition, the mean monthly CPUE generally declined during decreasing mean river discharge 

within the Lower San Joaquin River, South Delta, and Central Delta Seine regions from May to 

July, suggesting a positive correlation during the juvenile migration period (Moyle et al. 2004). 

We further examined the relationship between mean weekly CPUE and transformed discharge 

with simple linear regression models. Although the results were largely inconclusive, the mean 

weekly CPUE of Sacramento splittail during the 2010 and 2011 field seasons was positively 

correlated with mean weekly river discharge (Figure 63). The proportion of mean weekly CPUE 

variability explained by river discharge ranged from 18% to 44% among each seine region. The

strongest correlation was observed at the Lower San Joaquin River Seine Region with 

approximately 44% (n = 60, p-value = 0.01) of the variability in the mean weekly CPUE from 

May to July being explained by Delta discharge (Figure 63). Therefore there is evidence that the 

timing and magnitude of juveniles migrating downstream also is positively influenced by higher 

river discharge or other correlated environmental variables (e.g., lower temperatures). 

Fork Length Distributions

The FLs of Sacramento splittail captured at the Chipps Island Trawl Site generally ranged from 

45 to 325 mm during the 2010 and 2011 field seasons (Figure 64). However, all individuals 

captured at Chipps Island from October to May were > 90 mm (FL) and all individuals captured 

from June through August were < 90 mm (FL). Furthermore, nearly all individuals captured at 

the Sacramento and Mossdale Trawl sites and within all seine regions were < 60 mm (FL), 

particularly from April to July (Figures 65-70). These data suggest that the DJFMP captured 

primarily adults migrating upstream to spawn from November to January and juveniles were 
82

captured while migrating downstream into and through the Estuary from May to June post 

spawn. 

The DJFMP appears to be effectively sampling juvenile Sacramento splittail in all gear types, but 

adults were primarily captured by the Chipps Island MWTR. For beach seines, adult splittail may 

not readily occupy shallow (depth < 2 m) littoral habitat. In addition, adults may be able to avoid 

beach seines during sampling. Further investigation of seine efficiency is recommended to

determine the effectiveness of sampling adult Sacramento splittail in littoral habitats. The 

Sacramento and Mossdale trawls are ineffective in sampling adult splittail during their upstream 

migration based on the fact that these trawls are towed upstream and not downstream. During the

downstream migration of adults, individuals are likely able to avoid the trawls. Overall, the 

DJFMP appears to provide adequate information on the recruitment and migration of juvenile 

Sacramento splittail within the San Francisco Estuary and lower Sacramento and San Joaquin 

rivers.
83

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

0.00

0.02

0.04

0.06

0.08

0.10

0

200

400

600

800

a) Sacramento Splittail 1000

n = 87

2010

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

CPUE (fish/10,000 m

3

)

0.00

0.03

0.06

0.09

0.12

0.15

0.18

Mean Discharge (m

3/sec)

0

1000

2000

3000

4000

2001 2003 2005 2007 2009 2011

0.0

0.1

0.2

0.3

0.4

0.5

0.6

0

400

800

1200

1600

2000

b) Sacramento Splittail

n = 66

2011

c) Sacramento Splittail

Inter-Annual

Figure 58. Mean monthly and yearly CPUE of Sacramento splittail captured in mid-water trawls 

(MWTRs) at the Chipps Island Trawl Site, and mean monthly and yearly Delta discharge during 

the a) 2010, b) 2011, and c) 2000 through 2011 field seasons. Sample size (n) corresponds to 

total number of fish caught.
84

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

0.000

0.002

0.004

0.006

0.008

0.010

0

200

400

600

800

1000 a) Sacramento Splittail

2010

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

CPUE (fish/10,000 m

3

)

0.00

0.01

0.02

0.03

0.04

Mean Discharge (m

3/sec)

0

400

800

1200

1600

2000

2001 2003 2005 2007 2009 2011

0.000

0.015

0.030

0.045

0.060

0

200

400

600

800

1000

1200

MWTR, n = 4 

KDTR, n = 0

b) Sacramento Splittail

2011

c) Sacramento Splittail

Inter-Annual

MWTR, n =0 

KDTR, n = 1

Figure 59. Mean monthly and yearly CPUE of Sacramento splittail captured in mid-water 

(MWTRs) and Kodiak trawls (KDTRs) at the Sacramento Trawl Site, and mean monthly and 

yearly Sacramento River discharge at Freeport during the a) 2010, b) 2011, and c) 2000 through 

2011 field seasons. Sample size (n) corresponds to total number of fish caught.
85

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

0

4

8

12

16

20

0

40

80

120

a) Sacramento splittail 160

n = 4,021

2010

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

CPUE (fish/10,000 m

3

)

0

40

80

120

160

200

Mean Discharge (m

3/sec)

0

200

400

600

800

2004 2005 2006 2007 2008 2009 2010 2011

0

10

20

30

40

50

0

75

150

225

300

b) Sacramento splittail

n = 69,585

2011

c) Sacramento splittail

Inter-Annual

Figure 60. Mean monthly and yearly CPUE of Sacramento splittail captured in Kodiak trawls 

(KDTRs) at the Mossdale Trawl Site, and mean monthly and yearly San Joaquin River discharge 

at Vernalis during the a) 2010, b) 2011, and c) 2004 through 2011 field seasons. Sample size (n) 

corresponds to total number of fish caught.
86

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

0

5000

10000

15000

20000

25000

30000

0

200

400

600

800

a) Sacramento splittail 1000

n = 5,914

2010

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

CPUE (fish/10,000 m

3

)

0

40000

80000

120000

160000

Mean Discharge (m

3/sec)

0

600

1200

1800

2400

3000

3600

2001 2003 2005 2007 2009 2011

0

5000

10000

15000

20000

25000

0

300

600

900

1200

1500

1800

Region 1

Region 2

Region 3

Region 4

Region 5

Region 6

Delta Outflow

Vernalis

Freeport

b) Sacramento splittail

n = 45,462

2011

c) Sacramento splittail

Inter-Annual

Figure 61. Mean monthly and yearly CPUE of Sacramento splittail captured in beach seines at 

Regions 1-6, and mean monthly and yearly Sacramento River discharge at Freeport, San Joaquin 

River discharge at Vernalis, and Delta discharge during the a) 2010, b) 2011, and c) 2000 

through 2011 field seasons. Sample size (n) corresponds to total number of fish caught.
87

Log10(Mean Discharge (m3/sec))

1.8 2.0 2.2 2.4 2.6 2.8 3.0 3.2 3.4 3.6

CPUE (fish/10,000 m

3

)

0.000

0.075

0.150

0.225

0.300

0.375

2010

2011

r

2

 = 0.31

p-value = 0.04

Figure 62. Linear regressions of mean weekly CPUE of Sacramento splittail captured at the 

Chipps Island Trawl Site and mean weekly Delta discharge from November to January during 

the 2010 and 2011 field seasons. 

1.4 1.6 1.8 2.0 2.2 2.4 2.6 2.8

0

60000

120000

180000

240000

300000

2010

2011

a) Region 3

r

2

 = 0.24

p-value = 0.12

1.4 1.6 1.8 2.0 2.2 2.4 2.6 2.8

CPUE (fish/10,000 m

3

)

0

20000

40000

60000

80000

b) Region 4

r

2

 = 0.18

p-value = 0.24

Log10(Mean Discharge (m3/sec))

1.4 1.6 1.8 2.0 2.2 2.4 2.6 2.8

0

40000

80000

120000

160000 c) Region 5

r

2

 = 0.44

p-value = 0.01

Figure 63. Linear regressions of mean weekly CPUE of Sacramento splittail captured in beach 

seines in the a) Central Delta Seine Region (Region 3), b) South Delta Seine Region (Region 4) 

and c) Lower San Joaquin Seine Region (Region 5) and mean weekly San Joaquin River 

discharge at Vernalis from May to July during the during the 2010 and 2011 field seasons. 
88

a) Chipps Island Trawl Site

n = 87 fish

2010

50 100 150 200 250 300 350 400

0

1

2

3

4

b) Chipps Island Trawl Site

n = 66 fish

2011

Fork Lengths (mm)

50 100 150 200 250 300 350 400

Catch Count

0

1

2

3

4

Figure 64. Fork length distributions for Sacramento splittail captured in mid-water trawls 

(MWTRs) at the Chipps Island Trawl Site during the 2010 and 2011 field seasons.

a) Sacramento Trawl Site

 MWTR

n = 4 fish

2011

50 100 150 200 250 300

0

1

2

b) Sacramento Trawl Site

KDTR

n = 1 fish

2010

Fork Lengths (mm)

50 100 150 200 250 300

Catch Count

0

1

2

Figure 65. Fork length distributions for Sacramento splittail captured in mid-water (MWTRs)

and Kodiak trawls (KDTRs) at the Sacramento Trawls Site during the 2010 and 2011 field 

seasons. No splittail were captured in MWTR and KDTR at the Sacramento Trawl Site during 

the 2010 and 2011 field seasons, respectively.
89

a) Mossdale Trawl Site

n = 4,021 fish

2010

20 30 40 50 60 70

0

200

400

600

b) Mossdale Trawl Site

n = 69,585 fish

2011

Fork Lengths (mm)

20 30 40 50 60 70

Catch Count

0

2000

4000

6000

8000

Figure 66. Fork length distributions for Sacramento splittail captured in Kodiak trawls (KDTRs)

at the Mossdale Trawl Site during the 2010 and 2011 field seasons.
90

a) Region 1

n = 1,045 fish

2010

20 40 60 80 100 120

0

20

40

60

80

b) Region 2

n = 477 fish

2010

20 40 60 80 100 120

0

10

20

30

40

c) Region 3

n = 2,124 fish

2010

20 40 60 80 100 120

Catch Count

0

70

140

210

280

d) Region 4

n = 1,469 fish

2010

Fork Lengths (mm)

20 40 60 80 100 120

0

100

200

300

400

Figure 67. Fork length distributions for Sacramento splittail captured in beach seines within the 

Lower Sacramento River (Region 1), North Delta (Region 2), Central Delta (Region 3), and 

South Delta (Region 4) Seine regions during the 2010 field season.
91 Region 5

n = 799 fish

2010

Fork Lengths (mm)

20 40 60 80 100

Catch Count

0

20

40

60

80

Figure 68. Fork length distributions for Sacramento splittail captured in beach seines within the 

Lower San Joaquin River Seine Region (Region 5) during the 2010 field season.

a) Region 1

n = 4,267 fish

2011

20 40 60 80 100 120 140 160

0

100

200

300

400

500

b) Region 2

n = 7,488 fish

2011

20 40 60 80 100 120 140 160

Catch Count

0

200

400

600

800

c) Region 3

n = 19,009 fish

2011

20 40 60 80 100 120 140 160

0

700

1400

2100

2800

d) Region 4

n = 6,413 fish

2011

Fork Lengths (mm)

20 40 60 80 100 120 140 160

0

200

400

600

Figure 69. Fork length distributions for Sacramento splittail captured in beach seines within the 

Lower Sacramento River (Region 1), North Delta (Region 2), Central Delta (Region 3), and 

South Delta (Region 4) Seine regions during the 2011 field season.
92

a) Region 5

n = 8,235 fish

2011

20 40 60 80 100 120 140

0

200

400

600

800

b) Region 6

n = 49 fish

2011

20 40 60 80 100 120 140

Catch Count

0

2

4

6

8

Fork Lengths (mm)

Figure 70. Fork length distributions for Sacramento splittail captured in beach seines within the 

Lower San Joaquin River (Region 5) and San Francisco/San Pablo Bay (Region 6) Seine regions 

during the 2011 field season.

Threadfin Shad

We captured 6,155 and 8,004 threadfin shad during the 2010 and 2011 field seasons, respectively

(Tables A18 and A19).

Distribution and Relative Abundance

Threadfin shad were captured in nearly all seine regions and trawl sites during the 2010 and 2011 

field seasons (Tables A18 and A19). At the Chipps Island Trawl Site, individuals were generally 

captured from June to February with higher densities observed from October through December 

in 2010 and from November through December in 2011 (Figure 71). Threadfin shad were 

observed in most months at the Sacramento Trawl Site during both field seasons and the mean 

monthly CPUE peaked during November in 2010 and December in 2011 (Figure 72). The 

majority of all threadfin shad captured by DJFMP trawls in 2010 and 2011 were caught by the 

Mossdale KDTR. Although individuals were detected during all months of the field season, very 

low mean monthly CPUEs were observed in February through May (Figure 73). The mean 

monthly CPUE at the Mossdale Trawl Site peaked in August and December during the 2010 and 

2011 field season, respectively. The mean yearly CPUE at the Chipps Island and Sacramento 

Trawl sites reached the lowest levels since 2000 during the 2010 and 2011 field seasons (Figures 

71 and 72). Similarly, the mean yearly CPUE at the Mossdale Trawl Site was relatively low in 

2010 and 2011, and were comparable to the low catches observed in 2006 and 2007 (Figure 73).
93

Threadfin shad were captured in beach seines primarily from July through December during the 

2010 and 2011 field seasons (Figure 74). However, we did not capture threadfin shad at the San 

Francisco/San Pablo Seine Region in 2010. The mean monthly CPUE peaked within most seine 

regions from October through November during the 2010 field season and from September 

through October during the 2011 field season. The mean yearly CPUE estimates suggest that 

threadfin shad have generally been observed in higher densities within the Lower Sacramento 

River, Lower San Joaquin River and South Delta Seine regions relative to other seine regions 

since the 2000 field season. In general, the densities within most seine regions have declined 

considerably over the last decade (Figure 74). The relatively low densities and declines of 

threadfin shad observed by the DJFMP in most trawl sites and seine regions is consistent with 

the findings from other fish surveys and investigations within the San Francisco Estuary (e.g., 

Sommer et al. 2007; Contreras et al. 2012). 

The threadfin shad is an introduced and short lived (~2 years) warmwater species that is 

dependent on fresh water. Threadfin shad are distributed throughout the Central Valley within 

reservoirs, the Sacramento-San Joaquin River system, and the upper portions of San Francisco 

Estuary and adults spawn from April through June when water temperatures exceed 20°C

(Moyle 2002). Previous studies demonstrated that threadfin shad experience low survival within 

the Sacramento-San Joaquin Delta during the winter when water temperatures approach 8°C 

(Turner 1966). Therefore the low densities of threadfin shad observed during 2010 and 2011

from February to June at all trawl sites and seine regions may be, in part, the result of cool water 

temperatures, particularly during the month of January (Tables A21-A23). Based on the 

assumption that the survival of overwintering threadfin shad was likely poor within the Estuary 

during the 2010 and 2011 field seasons, we believe that most individuals captured by the DJFMP 

from July through January may have been individuals immigrating into the DJFMP sampling 

area from further upstream, particularly from the warmer San Joaquin River drainage. 

Influence of River Discharge

During the 2010 and 2011 field seasons, threadfin shad were typically not captured by the 

DJFMP from February to June during periods of relatively high river discharges, suggesting a 

very distinct negative flow relationship (Figures 71-74). However this relationship may have 

been in response to high mortality resulting from low water temperature. Therefore, we 

attempted to isolate the impact of discharge on threadfin shad CPUE by evaluating catch data 

from July to December when water temperatures were suitable and there was occupancy 

throughout most of the Estuary. The mean monthly CPUEs of threadfin shad at most trawl sites 

and within all seine regions showed little to no relationship to river discharge during the 2010 

and 2011 field seasons from July to January (Figures 71, 72, and 74). However, we did observe 

that the mean monthly CPUE of threadfin shad at the Mossdale Trawl Site declined during 

periods of lower mean river discharge in months following the spawning period (i.e., AugustOctober; Figure 73). Therefore, we developed a simple linear regression model to examine the 

influence of discharge at Vernalis (log10 transformed) on the mean weekly CPUE of threadfin 

shad at the Mossdale Trawl Site. Assuming a linear relationship, we demonstrated a significant 

negative correlation (p-value = 0.01) where 40% of the variability in the mean weekly CPUE 

from August to October was explained by river discharge (Figure 75). Therefore, there is some 

evidence that river discharge may have influenced the number of threadfin shad entering the 
94

Delta from the San Joaquin River during 2010 and 2011. Overall, our observations suggest that 

threadfin shad densities within the Estuary were likely mediated by a combination of limiting 

conditions (e.g., high river discharge, low temperatures, high salinity, and low turbidity; Moyle 

2002; Feyrer et al. 2007; MacNally et al. 2010) rather than solely river discharge (Dege and 

Brown 2004) during the 2010 and 2011 field seasons. 

Fork Length Distributions

The FLs of threadfin shad captured during the 2010 and 2011 field seasons generally ranged 

from 45 to 140 mm at the Chipps Island and Sacramento Trawl sites and from 25 to 160 mm at 

the Mossdale Trawl Site (Figures 76-78). The length-frequency distributions likely represented

three separate age classes (Moyle 2002). The FLs of threadfin shad within most seine regions 

ranged from 25 to 120 mm (Figures 79-82). The majority of threadfin shad < 50 mm (FL) were 

captured at the Mossdale Trawl Site and Lower San Joaquin River, Lower Sacramento River, 

North Delta, and South Delta Seine regions suggesting that only a small portion of the Estuary 

was used as rearing habitat. However, these results can be confounded by variable gear 

efficiencies and sample bias (Van Den Avyle et al. 1995). 
95

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

0.0

0.1

0.2

0.3

0.4

0.5

0.6

0

200

400

600

800

a) Threadfin shad 1000

n = 373

2010

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

CPUE (fish/10,000 m

3

)

0.0

0.3

0.6

0.9

1.2

1.5

Mean Discharge (m

3/sec)

0

1000

2000

3000

4000

2001 2003 2005 2007 2009 2011

0.0

0.5

1.0

1.5

2.0

2.5

0

400

800

1200

1600

2000

b) Threadfin shad

n = 408

2011

c) Threadfin shad

Inter-Annual

Figure 71. Mean monthly and yearly CPUE of threadfin shad captured in mid-water trawls 

(MWTRs) at the Chipps Island Trawl Site, and mean monthly and yearly Delta discharge during 

the a) 2010, b) 2011, and c) 2000 through 2011 field seasons. Sample size (n) corresponds to 

total number of fish caught.
96

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

0.0

0.3

0.6

0.9

1.2

1.5

0

200

400

600

800

a) Threadfin shad 1000

2010

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

CPUE (fish/10,000 m

3

)

0.0

0.1

0.2

0.3

0.4

Mean Discharge (m

3/sec)

0

400

800

1200

1600

2000

2001 2003 2005 2007 2009 2011

0.0

0.5

1.0

1.5

2.0

2.5

0

300

600

900

1200

MWTR, n = 11

KDTR, n = 64

b) Threadfin shad

2011

c) Threadfin shad

Inter-Annual

MWTR, n = 11

KDTR, n = 150

Figure 72. Mean monthly and yearly CPUE of threadfin shad captured in mid-water (MWTRs) 

and Kodiak trawls (KDTRs) at the Sacramento Trawl Site, and mean monthly and yearly 

Sacramento River discharge at Freeport during the a) 2010, b) 2011, and c) 2000 through 2011 

field seasons. Sample size (n) corresponds to total number of fish caught.
97

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

0

2

4

6

8

10

12

0

40

80

120

a) Threadfin shad 160

n = 1,773

2010

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

CPUE (fish/10,000 m

3

)

0

2

4

6

8

10

Mean Discharge (m

3/sec)

0

200

400

600

800

2004 2005 2006 2007 2008 2009 2010 2011

0

2

4

6

8

10

12

0

75

150

225

300

b) Threadfin shad

n = 1,786

2011

c) Threadfin shad

Inter-Annual

Figure 73. Mean monthly and yearly CPUE of threadfin shad captured in Kodiak trawls 

(KDTRs) at the Mossdale Trawl Site, and mean monthly and yearly San Joaquin River discharge 

at Vernalis during the a) 2010, b) 2011, and c) 2004 through 2011 field seasons. Sample size (n) 

corresponds to total number of fish caught.
98

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

0

2000

4000

6000

8000

10000

12000

0

200

400

600

800

a) Threadfin shad 1000

n = 3,845

2010

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

CPUE (fish/10,000 m

3

)

0

2000

4000

6000

8000

10000

12000

Mean Discharge (m

3/sec)

0

600

1200

1800

2400

3000

3600

2001 2003 2005 2007 2009 2011

0

2000

4000

6000

8000

10000

0

300

600

900

1200

1500

1800

Region 1

Region 2

Region 3

Region 4

Region 5

Region 6

Delta Outflow

Vernalis

Freeport

b) Threadfin shad

n = 5,732

2011

c) Threadfin shad

Inter-Annual

Figure 74. Mean monthly and yearly CPUE of threadfin shad captured in beach seines at Regions 

1-6, and mean monthly and yearly Sacramento River discharge at Freeport, San Joaquin River 

discharge at Vernalis, and Delta discharge during the a) 2010, b) 2011, and c) 2000 through 2011 

field seasons. Sample size (n) corresponds to total number of fish caught.
99

Log10(Mean Discharge (m3/sec))

1.0 1.2 1.4 1.6 1.8 2.0

CPUE (fish/10,000 m

3

)

0

5

10

15

20

25 2010

2011

r

2

 = 0.40

p-value = 0.01

Figure 75. Linear regressions of mean weekly CPUE of threadfin shad captured in Kodiak trawls

(KDTRs) at the Mossdale Trawl Site and mean weekly San Joaquin River discharge at Vernalis 

from August through October during the 2010 and 2011 field seasons. 

a) Chipps Island Trawl Site

n = 373 fish

2010

40 60 80 100 120 140 160 180

0

5

10

15

20

b) Chipps Island Trawl Site

n = 408 fish

2011

Fork Lengths (mm)

40 60 80 100 120 140 160 180

Catch Count

0

5

10

15

20

Figure 76. Fork length distributions for threadfin shad captured in mid-water trawls (MWTRs) at 

the Chipps Island Trawl Site during the 2010 and 2011 field seasons.
100

a) Sacramento Trawl Site

MWTR

n = 11 fish

2010

30 45 60 75 90 105 120 135

0

1

2

3

b) Sacramento Trawl Site

MWTR

n = 11 fish

2011

30 45 60 75 90 105 120 135

0

1

2

3

c) Sacramento Trawl Site

KDTR

n = 150 fish

2010

30 45 60 75 90 105 120 135

Catch Count

0

3

6

9

12

d) Sacramento Trawl Site

KDTR

n = 64 fish

2011

Fork Lengths (mm)

30 45 60 75 90 105 120 135

0

2

4

6

Figure 77. Fork length distributions for threadfin shad captured in mid-water (MWTRs) and 

Kodiak trawls (KDTRs) at the Sacramento Trawl Site during the 2010 and 2011 field seasons.
101

a) Mossdale Trawl Site

n = 1,773 fish

2010

30 45 60 75 90 105 120 135 150 165 180

0

20

40

60

80

b) Mossdale Trawl Site

n = 1,786 fish

2011

Fork Lengths (mm)

30 45 60 75 90 105 120 135 150 165 180

Catch Count

0

25

50

75

100

Figure 78. Fork length distributions for threadfin shad captured in Kodiak trawls (KDTRs) at the

Mossdale Trawl Site during the 2010 and 2011 field seasons.
102

a) Region 1

n = 1,275 fish

2010

40 60 80 100 120 140

0

20

40

60

80

b) Region 2

n = 203 fish

2010

40 60 80 100 120 140

0

4

8

12

16

c) Region 3

n = 255 fish

2010

40 60 80 100 120 140

Catch Count

0

10

20

30

d) Region 4

n = 2,059 fish

2010

Fork Lengths (mm)

40 60 80 100 120 140

0

60

120

180

240

Figure 79. Fork length distributions for threadfin shad captured in beach seines within the Lower 

Sacramento River (Region 1), North Delta (Region 2), Central Delta (Region 3), and South Delta 

(Region 4) Seine regions during the 2010 field season.
103 Region 5

n = 53 fish

2010

40 60 80 100 120 140

0

2

4

6

8 Catch Count

Fork Lengths (mm)

Figure 80. Fork length distributions for threadfin shad captured in beach seines within the Lower 

San Joaquin River Seine Region (Region 5) during the 2010 field season.

a) Region 1

n = 1,042 fish

2011

40 60 80 100 120 140 160

0

20

40

60

b) Region 2

n = 477 fish

2011

40 60 80 100 120 140 160

0

6

12

18

24

c) Region 3

n = 32 fish

2011

40 60 80 100 120 140 160

Catch Count

0

2

4

6

8

d) Region 4

n = 4,036 fish

2011

Fork Lengths (mm)

40 60 80 100 120 140 160

0

75

150

225

300

Figure 81. Fork length distributions for threadfin shad captured in beach seines within the Lower 

Sacramento River (Region 1), North Delta (Region 2), Central Delta (Region 3), and South Delta 

(Region 4) Seine regions during the 2011 field season.
104

a) Region 5

n = 174 fish

2011

40 60 80 100 120 140

0

4

8

12

16

b) Region 6

n = 1 fish

2011

40 60 80 100 120 140

Catch Count

0

1

2

3

Fork Lengths (mm)

Figure 82. Fork length distributions for threadfin shad captured in beach seines within the Lower 

San Joaquin River (Region 5) and San Francisco/San Pablo Bay (Region 6) Seine regions during 

the 2011 field season.

Striped Bass

A total of 1,085 and 591 striped bass were captured by the DJFMP during the 2010 and 2011 

field seasons, respectively (Tables A18 and A19).

Distribution and Relative Abundance

We captured striped bass at all trawl sites and within all seine regions during the 2010 and 2011 

field seasons (Tables A18 and A19). The majority of all striped bass captured by the DJFMP in 

2010 and 2011 were caught at the Chipps Island Trawl Site. Individuals were captured at Chipps 

Island during all months, but relatively low densities were observed from March through June 

(Figure 83). The mean monthly CPUE peaked at Chipps Island in October and August during the 

2010 and 2011 field seasons, respectively (Figure 83). The mean yearly CPUE at the Chipps 

Island Trawl Site reached the lowest levels since 2000 during the 2010 and 2011 field seasons

(Figure 83). Very few striped bass (total < 6) were observed at the Sacramento Trawl Site during 

the 2010 and 2011 field seasons (Figure 84). Individuals were captured by the Sacramento 

MWTR during the spring and summer. The mean yearly CPUE estimates suggest that striped 

bass captures at the Sacramento Trawl Site have been consistently low since the 2000 field 

season (Figure 84). At the Mossdale Trawl Site, striped bass monthly CPUE peaked in either 

July or August and few or no individuals were captured from February to July (Figure 85). The 

mean yearly CPUEs were relatively low at the Mossdale Trawl Site for the 2010 and 2011 field 

seasons and were less than a quarter of those observed during the 2008 and 2009 field seasons 

(Figure 85). 
105

Striped bass were primarily captured in beach seines from July through September during the 

2010 and 2011 field seasons (Figure 86). However, no individuals were observed within the 

Central Delta Seine Region in 2011. The mean monthly CPUE peaked within most seine regions 

in August or September. The North Delta, Lower San Joaquin River, and South Delta Seine 

regions showed the highest striped bass densities relative to other seine regions throughout much 

of the last decade. No discernible inter-annual trend in striped bass CPUE could be detected

within and among seine regions since the 2000 field season (Figure 86). 

The striped bass is a long-lived, introduced, anadromous, and iteroparous species (Moyle 2002). 

Adults generally occur within the lower portions of the San Francisco Estuary (e.g., San 

Francisco and San Pablo bays) and/or the Pacific Ocean throughout much of the year and

migrate upstream to spawn within or upstream of the lower Sacramento and San Joaquin rivers

from April to June (Turner and Chadwick 1972; Moyle 2002). After spawning, embryos and 

larval striped bass are often translocated by rivers to the Estuary where juveniles normally rear in 

and near the low salinity zone (Turner and Chadwick 1972; Moyle 2002; Sommer et al. 2011). 

The relative higher densities of striped bass at the Mossdale Trawl Site and within the North 

Delta and Lower San Joaquin River Seine regions from July to September during the 2010 and 

2011 field seasons was likely a result of juveniles migrating to the low salinity zone post spawn. 

Furthermore, the low densities or absence of striped bass from January to June at nearly all seine 

regions and trawl sites was likely due to most juveniles and sub-adults (i.e., individuals most 

susceptible to DJFMP sampling methods) occupying the low salinity zone which was located 

downstream of the Chipps Island Trawl Site (i.e., the majority of all DJFMP sampling locations) 

during the spring of both field seasons. Because the DJFMP does not sample the entire Estuary, 

the inter-annual abundance trends do not account for distribution shifts and the resulting bias is 

unknown (Kimmerer et al. 2001; Sommer et al. 2011).

Influence of River Discharge

During the 2010 and 2011 field seasons, striped bass were typically captured by the DJFMP from 

July to January during periods of relatively low river discharge, suggesting a distinct negative 

flow relationship (Figures 83-86). However this relationship was likely in response to high river 

discharges shifting the low salinity zone and hence the distribution of striped bass downstream of 

the DJFMP sampling locations (Turner and Chadwick 1972; Kimmerer et al. 2001; Sommer et 

al. 2011). Therefore, we attempted to isolate the effect of discharge on striped bass densities by 

evaluating catch data from June to September when the position of the low salinity zone was at 

or upstream of the Chipps Island Trawl Site and there were likely juveniles occurring within the 

Delta. The mean monthly CPUEs of striped bass at all trawl sites and within all seine regions 

showed no discernible relationship to river discharge during the 2010 and 2011 field seasons. As 

a result, these data suggest that the relative abundance of striped bass at DJFMP sampling 

locations within or upstream of the Delta was likely mediated by the timing and success of 

spawning adults and the location of the low salinity zone rather than river discharge (Stevens et 

al. 1985; Dege and Brown 2004). Previous investigations have suggested that river discharge

positively influences the abundance of juvenile striped bass (e.g., Turner and Chadwick 1972; 

Stevens 1977), however this relationship has greatly weakened since the 1970s (Kimmerer et al. 

2001). 
106

Fork Length Distributions

The majority of striped bass captured during the 2010 and 2011 field seasons ranged from 50 to 

150 mm (FL) at the Chipps Island Trawl Site (Figure 87) and from 25 to 125 mm (FL) at the 

Mossdale Trawl Site (Figure 88). At the Sacramento Trawl Site, the few individuals observed 

ranged from 100 to 500 mm in FL (Figure 89). In beach seines, the FLs of striped bass were 

typically less than 150 mm except within the San Francisco/San Pablo Bay Seine Region where 

individuals captured had FLs up to 300 mm (Figures 90-93). These data further support that the 

DJFMP captured primarily juveniles or sub-adults (age-0 or age-1; Moyle 2002) migrating into 

and rearing within the upper portions of the San Francisco Estuary from primarily July to 

October prior to the low salinity habitat shifting downstream into Suisun and/or San Pablo bays 

by increased river discharges. 

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

0.0

0.2

0.4

0.6

0.8

1.0

0

200

400

600

800

a) Striped bass 1000

n = 896

2010

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

CPUE (fish/10,000 m

3

)

0.0

0.1

0.2

0.3

0.4

0.5

0.6

Mean Discharge (m

3/sec)

0

1000

2000

3000

4000

2001 2003 2005 2007 2009 2011

0.0

0.5

1.0

1.5

2.0

0

400

800

1200

1600

2000

b) Striped bass

n = 308

2011

c) Striped bass

Inter-Annual

Figure 83. Mean monthly and yearly CPUE of striped bass captured in mid-water trawls 

(MWTRs) at the Chipps Island Trawl Site, and mean monthly and yearly Delta discharge during 

the a) 2010, b) 2011, and c) 2000 through 2011 field seasons. Sample size (n) corresponds to 

total number of fish caught.
107

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

0.00

0.02

0.04

0.06

0.08

0

200

400

600

800

a) Striped bass 1000

2010

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

CPUE (fish/10,000 m

3

)

0.0000

0.0075

0.0150

0.0225

0.0300

Mean Discharge (m

3/sec)

0

400

800

1200

1600

2000

2001 2003 2005 2007 2009 2011

0.000

0.005

0.010

0.015

0.020

0.025

0

300

600

900

1200

MWTR, n = 5

KDTR, n = 0

b) Striped bass

2011

c) Striped bass

Inter-Annual

MWTR, n = 3

KDTR, n = 0

Figure 84. Mean monthly and yearly CPUE of striped bass captured in mid-water (MWTRs) and 

Kodiak trawls (KDTRs) at the Sacramento Trawl Site, and mean monthly and yearly Sacramento 

River discharge at Freeport during the a) 2010, b) 2011, and c) 2000 through 2011 field seasons. 

Sample size (n) corresponds to total number of fish caught.
108

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

0.0

0.2

0.4

0.6

0.8

1.0

1.2

0

40

80

120

a) Striped bass 160

n = 127

2010

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

CPUE (fish/10,000 m

3

)

0.00

0.05

0.10

0.15

0.20

0.25

0.30

0.35

Mean Discharge (m

3/sec)

0

200

400

600

800

2004 2005 2006 2007 2008 2009 2010 2011

0.0

0.2

0.4

0.6

0.8

1.0

1.2

0

75

150

225

300

b) Striped bass

n = 55

2011

c) Striped bass

Inter-Annual

Figure 85. Mean monthly and yearly CPUE of striped bass captured in Kodiak trawls (KDTRs) 

at the Mossdale Trawl Site, and mean monthly and yearly San Joaquin River discharge at 

Vernalis during the a) 2010, b) 2011, and c) 2004 through 2011 field seasons. Sample size (n) 

corresponds to total number of fish caught.
109

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

0

200

400

600

800

1000

0

200

400

600

800

1000 a) Striped bass

n = 57

2010

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

CPUE (fish/10,000 m

3

)

0

200

400

600

800

1000

1200

Mean Discharge (m

3/sec)

0

600

1200

1800

2400

3000

3600

2001 2003 2005 2007 2009 2011

0

50

100

150

200

250

300

350

0

300

600

900

1200

1500

1800

Region 1

Region 2

Region 3

Region 4

Region 5

Region 6

Delta Outflow

Vernalis

Freeport

b) Striped bass

n = 225

2011

c) Striped bass

Inter-Annual

Figure 86. Mean monthly and yearly CPUE of striped bass captured in beach seines at Regions 

1-6, and mean monthly and yearly Sacramento River discharge at Freeport, San Joaquin River 

discharge at Vernalis, and Delta discharge during the a) 2010, b) 2011, and c) 2000 through 2011 

field seasons. Sample size (n) corresponds to total number of fish caught.
110

a) Chipps Island Trawl Site

n = 896 fish

2010

100 200 300 400 500 600

0

10

20

30

b) Chipps Island Trawl Site

n = 308 fish

2011

Fork Lengths (mm)

100 200 300 400 500 600

Catch Count

0

5

10

15

20

Figure 87. Fork length distributions for striped bass captured in mid-water trawls (MWTRs) at 

the Chipps Island Trawl Site during the 2010 and 2011 field seasons.

a) Mossdale Trawl Site

n = 127 fish

2010

50 100 150 200 250 300

0

3

6

9

12

15

b) Mossdale Trawl Site

n = 55 fish

2011

Fork Lengths (mm)

50 100 150 200 250 300

Catch Count

0

1

2

3

4

5

Figure 88. Fork length distributions for striped bass captured in Kodiak trawls (KDTRs) at the 

Mossdale Trawl Site during the 2010 and 2011 field seasons.
111

a) Sacramento Trawl Site

MWTR

n = 5 fish

2010

100 200 300 400 500

0

1

2

3

4

b) Sacramento Trawl Site

MWTR

n = 3 fish

2011

Fork Lengths (mm)

100 200 300 400 500

Catch Count

0

1

2

Figure 89. Fork length distributions for striped bass captured in mid-water (MWTRs) and Kodiak 

trawls (KDTRs) at the Sacramento Trawl Site during the 2010 and 2011 field seasons.
112

a) Region 1

n = 5 fish

2010

40 60 80 100 120 140 160

0

1

2

3

b) Region 2

n = 15 fish

2010

40 60 80 100 120 140 160

0

1

2

3

c) Region 3

n = 6 fish

2010

40 60 80 100 120 140 160

Catch Count

0

1

2

3

d) Region 4

n = 4 fish

2010

Fork Lengths (mm)

40 60 80 100 120 140 160

0

1

2

3

Figure 90. Fork length distributions for striped bass captured in beach seines within the Lower 

Sacramento River (Region 1), North Delta (Region 2), Central Delta (Region 3), and South Delta 

(Region 4) Seine regions during the 2010 field season.
113

a) Region 5

n = 24 fish

2010

50 100 150 200 250 300 350

0

1

2

3

4

5

b) Region 6

n = 3 fish

2010

Fork Lengths (mm)

50 100 150 200 250 300 350

Catch Count

0

1

2

3

Figure 91. Fork length distributions for striped bass captured in beach seines within the Lower 

San Joaquin River (Region 5) and San Francisco/San Pablo Bay (Region 6) Seine regions during 

the 2010 field season.
114

a) Region 1

n = 3 fish

2011

40 60 80 100 120 140 160

0

1

2

3

4

b) Region 2

n = 114 fish

2011

40 60 80 100 120 140 160

0

3

6

9

12

15

c) Region 4

n = 88 fish

2011

40 60 80 100 120 140 160

Catch Count

0

1

2

3

4

5

d) Region 5

n = 9 fish

2011

Fork Lengths (mm)

40 60 80 100 120 140 160

0

1

2

3

Figure 92. Fork length distributions for striped bass captured in beach seines within the Lower 

Sacramento River (Region 1), North Delta (Region 2), South Delta (Region 4), and Lower San 

Joaquin River (Region 5) Seine regions during the 2011 field season.
115 Region 6

n = 11 fish

2011

Fork Lengths (mm)

50 100 150 200 250 300 350

Catch Count

0

1

2

3

4

Figure 93. Fork length distributions for striped bass in beach seines within the San Francisco/San 

Pablo Bay Seine Region (Region 6) during the 2011 field season.
116

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122

APPENDIX
123

Table A1. Sites sampled during the 2010 field season categorized by gear or region. Station 

codes refer to body of water (first 2 letters; AR = American River, DS = Disappointment 

Slough, GS = Georgiana Slough, LP = Little Potato Slough, MK = Mokelumne River, MR = 

Middle River, MS = Mayberry Slough, OR = Old River, SA = San Francisco Bay, SB = 

Suisun Bay, SF = South Fork of Mokelumne River, SJ = San Joaquin River, SP=San Pablo 

Bay, SR = Sacramento River, SS = Steamboat Slough, TM = Three Mile Slough, WD = 

Werner Dredger Cut, or XC = Delta Cross Channel), river mile (3 digits), and location within 

site (last letter; N = north, S = south, W = west, E = east, or M = mid channel). For example, 

Colusa State Park is on the Sacramento River (SR) at river mile 144 on the west bank (W).

Site Code Site Name County

UTM Coordinates First Year 

Sampled 

Annually Zone Northing Easting

Region 1: Lower Sacramento River Seine

SR144W Colusa State Park Colusa 10 S 4341652 585032 1981

SR138E Ward's Landing Colusa 10 S 4338873 591787 1981

SR130E South Meridian Sutter 10 S 4329625 594819 1981

SR094E Reels Beach Sutter 10 S 4301235 610500 1981

SR090W Knight's Landing Yolo 10 S 4295506 610842 1981

SR080E* Verona Sutter 10 S 4293731 620049 1981

SR071E* Elkhorn Sacramento 10 S 4281359 619626 1981

Region 2: North Delta Seine

SR060E* Discovery Park Sacramento 10 S 4273503 629820 1976

AM001S* American River Sacramento 10 S 4273377 630121 1976

SR049E* Garcia Bend Sacramento 10 S 4259863 627056 1976

SR043W Clarksburg Yolo 10 S 4249352 629186 1976

SS011N Steamboat Slough Sacramento 10 S 4240586 624600 1992

SR024E Koket Sacramento 10 S 4233475 626473 1976

SR017E Isleton Sacramento 10 S 4224781 621633 1976

SR014W Rio Vista Solano 10 S 4227355 617119 1976

SR012W Sandy Beach Solano 10 S 4222029 614333 2007

MS001N Sherman Island Sacramento 10 S 4212733 606513 1976

Region 3: Central Delta Seine

SJ005N Eddo's Sacramento 10 S 4212249 614110 1976

SJ001S Antioch Dunes Contra Costa 10 S 4208157 606855 1979

XC001N Delta Cross Channel Sacramento 10 S 4234115 630930 1976

GS010E Georgiana Slough Sacramento 10 S 4231900 628914 1976

MK004W B&W Marina Sacramento 10 S 4220909 624418 1979

SF014E Wimpy's San Joaquin 10 S 4232068 632064 1976

TM001N Brannan Island Sacramento 10 S 4219577 615378 1976

DS002S King's Island San Joaquin 10 S 4213457 635248 1979

LP003E Terminous San Joaquin 10 S 4219075 631488 1979
124

Table A1. Continued.

Site Code Site Name County

UTM Coordinates First Year 

Sampled 

Annually Zone Northing Easting

Region 4: South Delta Seine

SJ051E Dos Reis San Joaquin 10 S 4188374 648601 1994

SJ041N Dad's Point San Joaquin 10 S 4202181 645287 1979

SJ032S Lost Isle San Joaquin 10 S 4206624 636393 1993

SJ026S Medford Island San Joaquin 10 S 4212589 630739 2002

OR023E Union Island San Joaquin 10 S 4187462 627498 1997

OR019E Old River San Joaquin 10 S 4193094 625167 1993

OR014W Cruiser Haven Contra Costa 10 S 4198087 626927 1993

OR003W Frank's Tract Contra Costa 10 S 4210312 624458 1993

MR010W Woodward Island San Joaquin 10 S 4198130 629336 1979

WD002W Veale Tract Contra Costa 10 S 4201793 622619 1993

Region 5: Lower San Joaquin River Seine

SJ083Wa N. of Tuolumne River Stanislaus 10 S 4164462 660960 1994

SJ077E a Route 132 Stanislaus 10 S 4167222 656395 1994

SJ074W aSturgeon Bend San Joaquin 10 S 4170903 654784 1994

SJ068W a Durham Site San Joaquin 10 S 4173594 652327 1994

SJ063W a Big Beach San Joaquin 10 S 4176666 650093 1994

SJ058Wab Wetherbeeab San Joaquin 10 S 4181923 649451 1994

SJ056Eab Mossdaleab San Joaquin 10 S 4183536 649043 1994

SJ079Eb San Luis Refuge Stanislaus 10 S 4166449 657914 2008

SJ076Wb N. of Route 132 Stanislaus 10 S 4168198 656679 2008

SJ074Ab Sturgeon Bend 

Alternate San Joaquin 10 S 4170228 654634 2008

Region 6: San Francisco and San Pablo Bay Seine

SA007E Berkeley Frontage Rd Alameda 10 S 4189562 561459 1997

SP001W China Camp Marin 10 S 4206179 546771 1997

SA009E Keller Beach Contra Costa 10 S 4196872 553964 1998

SP000W McNear's Beach Marin 10 S 4205405 547852 1997

SA008W Paradise Beach Marin 10 S 4194678 546872 1997

SP003E Point Pinole East Contra Costa 10 S 4206789 556219 1998

SA010W San Quentin Beach Marin 10 S 4199230 544068 1997

SA004W Tiburon Beach Marin 10 S 4193885 544413 1997

SA001M Treasure Island San Francisco 10 S 4185026 555671 1997
125

Table A1. Continued.

Site Code Site Name County

UTM Coordinates First Year 

Sampled 

Annually Zone Northing Easting

Region 7: Sacramento Area Seine

SR062E Sand Cove Sacramento 10 S 4273283 626860 1994

SR057E Miller Park Sacramento 10 S 4269001 629279 1994

SR055E Sherwood Harbor Sacramento 10 S 4265358 628190 1994

Trawls

SR055M Sacramento Sacramento 10 S 4265084 628299 1988

SJ054M Mossdale San Joaquin 10 S 4182898 649315 1996

SB055M,N,S Chipps Island Contra Costa 10 S 4211218 595531 1976

* Indicates site was also included within Region 7 from Oct 1st to Jan 31st for data analysis

a Indicates site was sampled when San Joaquin River discharge was > 51m3/s 

ab Indicates site was sampled throughout the year

b Indicates site was sampled when San Joaquin River discharge was ≤ 51m3/s
126

Table A2. Number of sample days and average number, standard deviation, and range of trawls 

per sample day for trawl sites within sample weeks during the 2010 field season.

Sample 

Week

Chipps Island (SB018M,N,S) Mossdale (SJ054M) Sacramento (SR055M)

Sample 

Days

Average 

Trawls per 

Sample Day 

(SD)

Range Sample 

Days

Average 

Trawls per 

Sample Day 

(SD)

Range Sample 

Days

Average 

Trawls per 

Sample Day 

(SD)

Range

8/2/2009 3 10 (0) 10 3 10 (0) 10 3 10 (0) 10

8/9/2009 3 10 (0) 10 3 10 (0) 10 3 10 (0) 10

8/16/2009 3 10 (0) 10 3 10 (0) 10 3 10 (0) 10

8/23/2009 3 10 (0) 10 3 8 (3.46) 4 - 10 3 10 (0) 10

8/30/2009 3 8.3 (1.53) 7 - 10 3 9.3 (1.15) 8 - 10 3 9 (1.73) 7 - 10

9/6/2009 3 10 (0) 10 3 10 (0) 10 3 10 (0) 10

9/13/2009 3 10 (0) 10 3 10 (0) 10 3 10 (0) 10

9/20/2009 3 10 (0) 10 3 10 (0) 10 3 10 (0) 10

9/27/2009 3 10 (0) 10 3 10 (0) 10 3 10 (0) 10

10/4/2009 3 8.3 (1.53) 7 - 10 3 9 (1.73) 7 - 10 3 9 (1.73) 7 - 10

10/11/2009 3 10 (0) 10 2 10 (0) 10 2 10 (0) 10

10/18/2009 3 10 (0) 10 3 10 (0) 10 3 10 (0) 10

10/25/2009 3 9.3 (0.58) 9 - 10 3 10 (0) 10 3 10 (0) 10

11/1/2009 3 10 (0) 10 3 10 (0) 10 3 10 (0) 10

11/8/2009 3 10 (0) 10 3 10 (0) 10 3 9.3 (1.15) 8 - 10

11/15/2009 3 10 (0) 10 3 8.7 (2.31) 6 - 10 3 10 (0) 10

11/22/2009 3 8.3 (2.89) 5 - 10 3 8.3 (2.89) 5 - 10 3 9 (1.73) 7 - 10

11/29/2009 3 9.7 (0.58) 9 - 10 3 9.3 (1.15) 8 - 10 3 10 (0) 10

12/6/2009 3 9.3 (1.15) 8 - 10 3 10 (0) 10 3 10 (0) 10

12/13/2009 3 11 (3.61) 8 - 15 3 10 (0) 10 3 10 (0) 10

12/20/2009 3 10 (0) 10 2 9.5 (0.71) 9 - 10 2 10 (0) 10

12/27/2009 3 9.7 (0.58) 9 - 10 3 8.7 (2.31) 6 - 10 3 8.3 (2.89) 5 - 10

1/3/2010 3 10 (0) 10 3 10 (0) 10 3 10 (0) 10

1/10/2010 3 10 (0) 10 3 10 (0) 10 3 10 (0) 10

1/17/2010 1 10 (0) 10 2 6.5 (4.95) 3 - 10 0 - -

1/24/2010 3 10 (0) 10 3 9.3 (1.15) 8 - 10 2 9.5 (0.71) 9 - 10

1/31/2010 3 10 (0) 10 3 10 (0) 10 3 10 (0) 10

2/7/2010 3 10 (0) 10 3 10 (0) 10 3 9.7 (0.58) 9 - 10

2/14/2010 3 10 (0) 10 3 10 (0) 10 3 8 (1.73) 7 - 10

2/21/2010 3 10 (0) 10 3 10 (0) 10 3 10 (0) 10

2/28/2010 3 10 (0) 10 3 10 (0) 10 3 10 (0) 10

3/7/2010 3 10 (0) 10 3 10 (0) 10 3 10 (0) 10

3/14/2010 3 10 (0) 10 3 8.7 (2.31) 6 - 10 3 10 (0) 10

3/21/2010 3 10 (0) 10 3 9 (1.73) 7 - 10 3 10 (0) 10

3/28/2010 3 10 (0) 10 4 10.3 (0.50) 10 - 11 3 10 (0) 10

4/4/2010 3 10 (0) 10 5 10.4 (0.89) 10 - 12 3 9.3 (1.15) 8 - 10

4/11/2010 3 9.3 (0.58) 9 - 10 5 9.6 (0.89) 8 - 10 3 10 (0) 10

4/18/2010 3 10 (0) 10 5 10 (0) 10 3 8.7 (2.31) 6 - 10

4/25/2010 3 10 (0) 10 4 10.25 (0.5) 10 - 11 3 10 (0) 10

5/2/2010 3 10 (0) 10 5 10 (0) 10 2 10 (0) 10

5/9/2010 3 9.7 (0.58) 9 - 10 5 10 (0) 10 2 10 (0) 10

5/16/2010 3 10 (0) 10 5 10.2 (0.45) 10 - 11 2 10 (0) 10

5/23/2010 3 8.7 (2.31) 6 - 10 5 10 (0) 10 2 10 (0) 10

5/30/2010 3 10 (0) 10 4 11.25 (2.50) 10 - 15 2 10 (0) 10

6/6/2010 3 10 (0) 10 3 10 (0) 10 2 8.5 (2.12) 7 - 10

6/13/2010 3 8.3 (2.89) 5 - 10 3 10.7 (0.58) 10 - 11 2 10 (0) 10

6/20/2010 3 10 (0) 10 2 10 (0) 10 2 10 (0) 10

6/27/2010 3 8.7 (2.31) 6 - 10 3 9.3 (1.15) 8 - 10 2 10 (0) 10

7/4/2010 3 10 (0) 10 3 10 (0) 10 3 10 (0) 10

7/11/2010 2 10 (0) 10 2 10 (0) 10 2 10 (0) 10

7/18/2010 3 9.3 (1.15) 8 - 10 3 10 (0) 10 3 10 (0) 10
127

Table A3. Number of sample days and average number, standard deviation, and range of 

trawls per sample day for trawl sites within sample weeks during the 2011 field season.

Sample 

Week

Chipps Island (SB018M,N,S) Mossdale (SJ054M) Sacramento (SR055M)

Sample 

Days

Average 

Trawl per 

Sample Day 

(SD)

Range Sample 

Days

Average 

Trawl per 

Sample Day 

(SD)

Range Sample 

Days

Average 

Trawl per 

Sample Day 

(SD)

Range

8/1/2010 3 10 (0) 10 3 10 (0) 10 3 10 (0) 10

8/8/2010 3 8.7 (2.3) 6-10 3 10 (0) 10 3 9.7 (0.6) 9-10

8/15/2010 3 8.3 (2.9) 5-10 3 10 (0) 10 3 10 (0) 10

8/22/2010 3 9.7 (0.6) 9-10 3 10 (0) 10 3 10 (0) 10

8/29/2010 3 8.7 (2.3) 6-10 3 9.3 (1.2) 8-10 3 8.7 (2.3) 6-10

9/5/2010 3 10 (0) 10 3 10 (0) 10 3 10 (0) 10

9/12/2010 3 10 (0) 10 3 10 (0) 10 3 10 (0) 10

9/19/2010 3 9 (1.7) 7-10 3 10 (0) 10 3 10 (0) 10

9/26/2010 3 10 (0) 10 3 10 (0) 10 3 9 (1) 8-10

10/3/2010 3 8.3 (2.9) 5-10 3 8.7 (1.5) 7-10 3 9 (1.7) 7-10

10/10/2010 3 10 (0) 10 3 10 (0) 10 3 8 (3.5) 4-10

10/17/2010 3 10 (0) 10 3 10 (0) 10 3 10 (0) 10

10/24/2010 3 10 (0) 10 3 10 (0) 10 3 10 (0) 10

10/31/2010 3 9.3 (1.2) 8-10 3 10 (0) 10 3 10 (0) 10

11/7/2010 3 10 (0) 10 3 10 (0) 10 3 10 (0) 10

11/14/2010 3 10 (0) 10 3 10 (0) 10 3 10 (0) 10

11/21/2010 3 8.3 (2.9) 5-10 3 8.3 (2.9) 5-10 3 8 (3.5) 4-10

11/28/2010 3 9 (1) 8-10 3 9.3 (1.2) 8-10 3 10 (0) 10

12/5/2010 3 9 (1.7) 7-10 3 10 (0) 10 3 8.3 (2.9) 5-10

12/12/2010 3 10 (0) 10 3 10 (0) 10 3 9.7 (0.6) 9-10

12/19/2010 3 8.3 (2.9) 5-10 2 9 (1.4) 8-10 2 5.5 (3.5) 3-8

12/26/2010 2 10 (0) 10 2 10 (0) 10 2 6 (1.4) 5-7

1/2/2011 3 9.3 (1.2) 8-10 3 9.3 (1.2) 8-10 3 10 (0) 10

1/9/2011 3 10 (0) 10 3 10 (0) 10 3 10 (0) 10

1/16/2011 3 10 (0) 10 3 9.3 (1.2) 8-10 3 10 (0) 10

1/23/2011 3 8 (1.7) 7-10 2 8 (2.8) 6-10 2 7.5 (3.5) 5-10

1/30/2011 3 10 (0) 10 3 9.7 (0.6) 9-10 3 8.7 (1.5) 7-10

2/6/2011 3 10 (0) 10 3 10 (0) 10 3 10 (0) 10

2/13/2011 3 10 (0) 10 3 10 (0) 10 3 10 (0) 10

2/20/2011 3 10 (0) 10 3 10 (0) 10 3 9 (1.7) 7-10

2/27/2011 3 10 (0) 10 3 10 (0) 10 3 10 (0) 10

3/6/2011 3 10 (0) 10 3 10 (0) 10 3 9.3 (1.2) 8-10

3/13/2011 3 10 (0) 10 3 9.7 (0.6) 9-10 3 9 (1.7) 7-10

3/20/2011 3 10 (0) 10 2 10 (0) 10 2 9.5 (0.7) 9-10

3/27/2011 3 10 (0) 10 3 10 (0) 10 3 10 (0) 10

4/3/2011 3 10 (0) 10 5 10 (0) 10 3 7.7 (4.0) 3-10

4/10/2011 3 10 (0) 10 5 10 (0) 10 3 10 (0) 10

4/17/2011 3 10 (0) 10 5 10 (0) 10 3 8.7 (2.3) 6-10

4/24/2011 3 10 (0) 10 5 10 (0) 10 3 10 (0) 10

5/1/2011 3 10 (0) 10 5 9.2 (1.8) 6-10 2 10 (0) 10

5/8/2011 3 10 (0) 10 6 13.3 (2.6) 10-15 2 10 (0) 10

5/15/2011 3 10 (0) 10 7 13.9 (3) 7-15 2 9.5 (0.7) 9-10

5/22/2011 3 7.7 (2.1) 6-10 6 13.3 (2.6) 10-15 2 10 (0) 10

5/29/2011 3 10 (0) 10 5 10.2 (0.4) 10-11 2 10 (0) 10

6/5/2011 3 10 (0) 10 5 9.8 (1.8) 7-12 2 10 (0) 10

6/12/2011 3 10 (0) 10 5 10 (0) 10 2 10 (0) 10

6/19/2011 3 10 (0) 10 3 10 (0) 10 2 10 (0) 10

6/26/2011 3 8.7 (2.3) 6-10 2 10 (0) 10 2 10 (0) 10

7/3/2011 3 10 (0) 10 3 10 (0) 10 3 10 (0) 10

7/10/2011 3 10 (0) 10 3 10 (0) 10 3 10 (0) 10

7/17/2011 3 10 (0) 10 3 10 (0) 10 3 10 (0) 10

7/24/2011 3 7 (5.2) 1-10 3 10 (0) 10 3 10 (0) 10
128

Table A4. Sample weeks that fish samples were collected at least once at seine 

sites in the Lower Sacramento River Region during the 2010 field season.

Sample 

Week

Station Code

SR144W SR138E SR130E SR094E SR090W SR080E SR071E

8/2/2009 X X X X X

8/9/2009 X X X X X X

8/16/2009 X X X X X

8/23/2009 X X X X X

8/30/2009 X X X X X

9/6/2009 X X X X X

9/13/2009 X X X X X

9/20/2009 X X X X X

9/27/2009 X X X X X X

10/4/2009 X X X X

10/11/2009 X X X X X X

10/18/2009 X X X X X X X

10/25/2009 X X X X X

11/1/2009 X X X X X X

11/8/2009 X X X X X

11/15/2009 X X X X

11/22/2009 X X X X

11/29/2009 X X X X

12/6/2009 X X X

12/13/2009 X X X X X

12/20/2009 X X X X X

12/27/2009 X X X X X

1/3/2010 X X X X X

1/10/2010 X X X X X X

1/17/2010 X X X

1/24/2010 X X X X X

1/31/2010 X X X X

2/7/2010 X X X X X

2/14/2010 X X X X X X

2/21/2010 X X X X X X

2/28/2010 X X X X X

3/7/2010 X X X X X

3/14/2010 X X X X X

3/21/2010 X X X X X X

3/28/2010 X X X X X

4/4/2010 X X X X X X X

4/11/2010 X X X X X

4/18/2010 X X X X X

4/25/2010 X X X X X

5/2/2010 X X X X

5/9/2010 X X X X

5/16/2010 X X X

5/23/2010 X X X X

5/30/2010 X X X X X

6/6/2010 X X X X X

6/13/2010 X X X X X

6/20/2010 X X X X

6/27/2010 X X X X

7/4/2010

7/11/2010

7/18/2010 X X X X X X

7/25/2010 X X X X X X X
129

Table A5. Sample weeks that fish samples were collected at least once at seine 

sites in the Lower Sacramento River Region during the 2011 field season.

Sample 

Week

Station Code

SR144W SR138E SR130E SR094E SR090W SR080E SR071E

8/1/2010 X X X X X X X

8/8/2010 X X X X X

8/15/2010 X X X X X X X

8/22/2010 X X X X X

8/29/2010 X X X X X X X

9/5/2010 X X X X X

9/12/2010 X X X X X X X

9/19/2010 X X X X X X

9/26/2010 X X X X X X

10/3/2010 X X X X X

10/10/2010 X X X X X X

10/17/2010 X X X X

10/24/2010 X X X X X X

10/31/2010 X X X X X X

11/7/2010 X X X X X X X

11/14/2010 X X X X X X X

11/21/2010 X X X X X X X

11/28/2010 X X X X X X

12/5/2010 X X X X X

12/12/2010 X X X X X

12/19/2010 X X X X X

12/26/2010 X X X X X

1/2/2011 X X X X X

1/9/2011 X X X X X X

1/16/2011 X X X X X

1/23/2011 X X X X X X

1/30/2011 X X X X X

2/6/2011 X X X X X

2/13/2011 X X X X X

2/20/2011 X X X X X X X

2/27/2011 X X X X X X X

3/6/2011 X X X X X X

3/13/2011 X X X X X X

3/20/2011 X X X X X

3/27/2011 X X X X X

4/3/2011 X X X X

4/10/2011 X X X

4/17/2011 X X X X X

4/24/2011 X X X X X X

5/1/2011 X X X X X X X

5/8/2011 X X X X X X X

5/15/2011 X X X X

5/22/2011 X X X X X X

5/29/2011 X X X X X X

6/5/2011 X X X X X

6/12/2011 X X X X X X X

6/19/2011 X X X X X X

6/26/2011 X X X

7/3/2011 X X X X X X X

7/10/2011 X X X X X

7/17/2011 X X X X X X

7/24/2011 X X X X X X
130

Table A6. Sample weeks that fish samples were collected at least once at seine sites in the 

North Delta Region during the 2010 field season.

Sample 

Week

Station Code

SR060E AM001S SR049E SR043W SS011N SR024E SR017E SR014W SR012W MS001N

8/2/2009 X X X X X X X X

8/9/2009 X X X X X X X X X

8/16/2009 X X X X X X X X X X

8/23/2009 X X X X X X X X X X

8/30/2009 X X X X X X X

9/6/2009 X X X X X X X X X X

9/13/2009 X X X X X X X

9/20/2009 X X X X X X X X X

9/27/2009 X X X X X X X X X X

10/4/2009 X X X X X X X X X X

10/11/2009 X X X X X X X X X X

10/18/2009 X X X X X X X X X X

10/25/2009 X X X X X X X X X

11/1/2009 X X X X X X X X X

11/8/2009 X X X X X X X X X

11/15/2009 X X X X X X X X X

11/22/2009 X X X X X X X X X

11/29/2009 X X X X X X X X X

12/6/2009 X X X X X X X X X X

12/13/2009 X X X X X X X X X X

12/20/2009 X X X X X X X X X X

12/27/2009 X X X X X X X X X X

1/3/2010 X X X X X X X X X X

1/10/2010 X X X X X X X X X X

1/17/2010 X X X X X X X X X

1/24/2010 X X X X X X X X X X

1/31/2010 X X X X X X X X X X

2/7/2010 X X X X X X X X X

2/14/2010 X X X X X X X X X X

2/21/2010 X X X X X X X X X

2/28/2010 X X X X X X X X X X

3/7/2010 X X X X X X X X

3/14/2010 X X X X X X X

3/21/2010 X X X X X X X X X X

3/28/2010 X X X X X X X X X X

4/4/2010 X X X X X X X X X X

4/11/2010 X X X X X X X X X X

4/18/2010 X X X X X X X X

4/25/2010 X X X X X X X X X

5/2/2010 X X X X X X X X X

5/9/2010 X X X X X X X

5/16/2010 X X X X X X X X X X

5/23/2010 X X X X X X X X

5/30/2010 X X X X X X X

6/6/2010 X X X X X X X X X

6/13/2010 X X X X X X X X

6/20/2010 X X X X X X X X X

6/27/2010 X X X X X X X

7/4/2010

7/11/2010 X X X

7/18/2010 X X X X X X X X

7/25/2010 X X X X X X X X X
131

Table A7. Sample weeks that fish samples were collected at least once at seine sites in the 

North Delta Region during the 2011 field season.

Sample 

Week

Station Code

SR060E AM001S SR049E SR043W SS011N SR024E SR017E SR014W SR012W MS001N

8/1/2010 X X X X X X X X X X

8/8/2010 X X X X X X X X X X

8/15/2010 X X X X X X X X X X

8/22/2010 X X X X X X X X X X

8/29/2010 X X X X X X X X X X

9/5/2010 X X X X X X X X X

9/12/2010 X X X X X X X X X X

9/19/2010 X X X X X X X X X X

9/26/2010 X X X X X X X X X X

10/3/2010 X X X X X X X X X X

10/10/2010 X X X X X X

10/17/2010 X X X X X X X X X X

10/24/2010 X X X X X X

10/31/2010 X X X X X X X X X X

11/7/2010 X X X X X X X X X X

11/14/2010 X X X X X X X X X X

11/21/2010 X X X X X X X X X X

11/28/2010 X X X X X X X X X X

12/5/2010 X X X X X X X X X X

12/12/2010 X X X X X X X X X X

12/19/2010 X X X X X X X X

12/26/2010 X X X X X X X X

1/2/2011 X X X X X X X X X X

1/9/2011 X X X X X X X X

1/16/2011 X X X X X X X X X X

1/23/2011 X X X X X X X X X

1/30/2011 X X X X X X X X X

2/6/2011 X X X X X X

2/13/2011 X X X X X X X X X

2/20/2011 X X X X X X X X

2/27/2011 X X X X X X X X X X

3/6/2011 X X X X X X X X X X

3/13/2011 X X X X X X X X X

3/20/2011 X X X X X X X X X

3/27/2011 X X X X X X X X

4/3/2011 X X X X X X X X X

4/10/2011 X X X X X X X

4/17/2011 X X X X X X X X

4/24/2011 X X X X X X X X X

5/1/2011 X X X X X X X X

5/8/2011 X X X X X X X X X

5/15/2011 X X X X X X X X

5/22/2011 X X X X X X X X

5/29/2011 X X X X X X X X X

6/5/2011 X X X X X X X X X X

6/12/2011 X X X X X X X X X

6/19/2011 X X X X X X X X X

6/26/2011 X X X X X X X X X

7/3/2011 X X X X X X X X

7/10/2011 X X X X X X X

7/17/2011 X X X X X X X

7/24/2011 X X X X X X X X X X
132

Table A8. The number of juvenile fish samples collected (i.e., number of days 

samples were collected) at seine sites by sample week in the Sacramento Area 

Beach Seine Region during the 2010 field season.

Sample Week Station Code

SR080E SR071E SR062E SR060E AM001S SR057E SR055E SR049E

9/27/2009 1 1 2 2 1 2

10/4/2009 3 3 3 3 1 3 3 3

10/11/2009 2 2 2 1 1 1 1 1

10/18/2009 3 3 3 3 1 3 3 3

10/25/2009 3 3 3 3 1 3 3 3

11/1/2009 3 3 2 3 1 3 2 3

11/8/2009 3 3 3 3 1 3 2 3

11/15/2009 3 3 3 3 1 3 3 3

11/22/2009 3 3 3 3 1 3 3 3

11/29/2009 3 3 3 3 1 3 3 2

12/6/2009 3 3 3 3 1 3 3 3

12/13/2009 3 3 3 3 1 3 3 3

12/20/2009 2 2 2 2 1 2 2 2

12/27/2009 2 2 2 2 1 2 2 2

1/3/2010 3 3 3 3 1 3 3 3

1/10/2010 1 1 1 1 1 1 1 1

1/17/2010 1 1 1 1 1

1/24/2010 1 1 1 1 1 1
133

Table A9. The number of juvenile fish samples collected (i.e., number of days 

samples were collected) at seine sites by sample week in the Sacramento Area 

Beach Seine Region during the 2011 field season.

Sample Week Station Code

SR080E SR071E SR062E SR060E AM001S SR057E SR055E SR049E

9/26/2010 1 2 1 2 2 1 1 1

10/3/2010 3 3 2 3 1 3 3 3

10/10/2010 3 3 3 3 1 3 3 2

10/17/2010 3 3 2 3 1 3 3 3

10/24/2010 3 3 3 3 1 3 3 3

10/31/2010 3 3 2 3 1 3 3 2

11/7/2010 3 3 2 2 1 3 3 3

11/14/2010 3 3 3 3 1 3 3 3

11/21/2010 3 3 2 3 1 3 3 3

11/28/2010 3 3 3 3 1 3 3 3

12/5/2010 3 3 3 3 1 3 3 3

12/12/2010 3 3 2 3 1 3 2 3

12/19/2010 1 1 1 1 1 1

12/26/2010 3 2 1 3

1/2/2011 3 2 1 2 1 2 3

1/9/2011 1 1 1 1 1 1

1/16/2011 1 1 1 1 1 1 1 1

1/23/2011 1 1 1 1 1 1 1 1
134

Table A10. Sample weeks that fish samples were collected at least once at seine sites 

in the Central Delta Region during the 2010 field season.

Sample 

Week

Station Code

SJ005N SJ001S XC001N GS010E MK004W SF014E TM001N DS002S LP003E

8/2/2009 X X X X X X X

8/9/2009 X X X X X X X X X

8/16/2009 X X X X X X X

8/23/2009 X X X X X X X

8/30/2009 X X X X X X X

9/6/2009 X X X X X X

9/13/2009 X X X X X X

9/20/2009 X X X X X X X X

9/27/2009 X X X X X X X X

10/4/2009 X X X X X X X X

10/11/2009 X X X X X X X

10/18/2009 X X X X X X

10/25/2009 X X X X X X

11/1/2009 X X X X X X X

11/8/2009 X X X X X X X

11/15/2009 X X X X X X X X

11/22/2009 X X X X X X X X X

11/29/2009 X X X X X X

12/6/2009 X X X X X X X X X

12/13/2009 X X X X X X X

12/20/2009 X X X X X X

12/27/2009 X X X X X X

1/3/2010 X X X X X X X X X

1/10/2010 X X X X X X

1/17/2010 X X X X X X X X

1/24/2010 X X X X X X

1/31/2010 X X X X X X X

2/7/2010 X X X X X X X

2/14/2010 X X X X X X X X X

2/21/2010 X X X X X X X

2/28/2010 X X X X X X

3/7/2010 X X X X X X X

3/14/2010 X X X X X X

3/21/2010 X X X X X X

3/28/2010 X X X X X X X X

4/4/2010 X X X X X X X

4/11/2010 X X X X X X X X

4/18/2010 X X X X X X X

4/25/2010 X X X X X X X X

5/2/2010 X X X X X X

5/9/2010 X X X X X X X

5/16/2010 X X X X X

5/23/2010 X X X X X X X

5/30/2010 X X X X X X X X

6/6/2010 X X X X X X X X

6/13/2010 X X X X X X X

6/20/2010 X X X X X X X X

6/27/2010 X X X X X X X X

7/4/2010

7/11/2010 X X X X X X

7/18/2010 X X X X X X X X X

7/25/2010 X X X X X X X
135

Table A11. Sample weeks that fish samples were collected at least once at seine sites 

in the Central Delta Region during the 2011 field season.

Sample 

Week

Station Code

SJ005N SJ001S XC001N GS010E MK004W SF014E TM001N DS002S LP003E

8/1/2010 X X X X X X X X

8/8/2010 X X X X X X X X

8/15/2010 X X X X X X X X

8/22/2010 X X X X X X

8/29/2010 X X X X X X X X

9/5/2010 X X X X X X X

9/12/2010 X X X X X X X X X

9/19/2010 X X X X X X X X

9/26/2010 X X X X X X X

10/3/2010 X X X X X X X X X

10/10/2010 X X X X X X

10/17/2010 X X X X X X X X X

10/24/2010 X X X X X

10/31/2010 X X X X X X X X X

11/7/2010 X X X X X X X X

11/14/2010 X X X X X X X X X

11/21/2010 X X X X X X

11/28/2010 X X X X X X X X

12/5/2010 X X X X X X

12/12/2010 X X X X X X X

12/19/2010 X X X X X X

12/26/2010 X X X X X X X

1/2/2011 X X X X X X

1/9/2011 X X X X X X X

1/16/2011 X X X X X X X X

1/23/2011 X X X X X X X

1/30/2011 X X X X X X X

2/6/2011 X X X X X

2/13/2011 X X X X X X

2/20/2011 X X X X X X X

2/27/2011 X X X X X X X X X

3/6/2011 X X X X X X X X

3/13/2011 X X X X X X X

3/20/2011 X X X X X X X

3/27/2011 X X X X X X X

4/3/2011 X X X X X

4/10/2011 X X X X X X X X

4/17/2011 X X X X X X X

4/24/2011 X X X X X X X

5/1/2011 X X X X X X X X

5/8/2011 X X X X X X X

5/15/2011 X X X X X X X

5/22/2011 X X X X X X X

5/29/2011 X X X X X X X

6/5/2011 X X X X X X X

6/12/2011 X X X X X X X X

6/19/2011 X X X X X X

6/26/2011 X X X X X X X X

7/3/2011 X X X X X

7/10/2011 X X X X X X X

7/17/2011 X X X X X X X

7/24/2011 X X X X X X X
136

Table A12. Sample weeks that fish samples were collected at least once at seine sites in 

the South Delta Region during the 2010 field season.

Sample 

Week

Station Code

SJ051E SJ041N SJ032S SJ026S OR023E OR019E OR014W OR003W WD002W MR010W

8/2/2009 X X X X X X X X

8/9/2009 X X X X X X

8/16/2009 X X X

8/23/2009 X X X X X X X X

8/30/2009 X X X X X

9/6/2009 X X X X

9/13/2009 X X X X X

9/20/2009 X X X X X X X

9/27/2009 X X X X X X X

10/4/2009 X X X X X

10/11/2009

10/18/2009 X X X X

10/25/2009

11/1/2009 X X X X X X X

11/8/2009 X X X X

11/15/2009 X X X X X X X X X

11/22/2009 X X X X X

11/29/2009 X X X X X X X

12/6/2009 X X X

12/13/2009 X X X X X

12/20/2009 X X

12/27/2009 X X X X

1/3/2010 X X X X

1/10/2010 X X X X X X X

1/17/2010 X

1/24/2010 X X X X

1/31/2010 X X X X X X

2/7/2010 X X X X X X X

2/14/2010 X X X X

2/21/2010 X X X X X X X X

2/28/2010 X X

3/7/2010 X X X X X X X

3/14/2010 X X X X X X X X X X

3/21/2010 X X X X

3/28/2010 X X X X

4/4/2010 X X X

4/11/2010 X X X X X X X

4/18/2010 X X X X X

4/25/2010 X X

5/2/2010 X X X X X

5/9/2010 X X X X X

5/16/2010 X X X X

5/23/2010 X X X X X X

5/30/2010 X X X X X

6/6/2010 X X X X X X X

6/13/2010 X X X

6/20/2010 X X X X X X X X

6/27/2010 X X X X

7/4/2010 X X X X X X X

7/11/2010

7/18/2010 X X X X X X X X

7/25/2010 X X X
137

Table A13. Sample weeks that fish samples were collected at least once at seine sites in the 

South Delta Region during the 2011 field season.

Sample 

Week

Station Code

SJ051E SJ041N SJ032S SJ026S OR023E OR019E OR014W OR003W WD002W MR010W

8/1/2010 X X X X X X X X X

8/8/2010 X X

8/15/2010 X X X X X X X X X

8/22/2010 X X X X X X X X

8/29/2010 X X X X X X

9/5/2010 X X

9/12/2010 X X X X X X X X

9/19/2010 X X X X X

9/26/2010 X X X X X X X

10/3/2010 X X X X X X X X

10/10/2010 X X X X X X X X

10/17/2010 X X X X X X X

10/24/2010 X X X X X X

10/31/2010 X X X X X X X

11/7/2010 X X X X

11/14/2010 X X X X X

11/21/2010 X X X

11/28/2010 X X X X X X

12/5/2010 X X X X X X

12/12/2010 X X X

12/19/2010 X X X X X

12/26/2010 X

1/2/2011 X X X X X X

1/9/2011 X X X X

1/16/2011 X X X X X X X X

1/23/2011 X X

1/30/2011 X X

2/6/2011 X X X

2/13/2011 X X X X

2/20/2011 X

2/27/2011 X X X X X X X X X X

3/6/2011 X X X

3/13/2011 X X X X X X X

3/20/2011

3/27/2011 X X X X X X

4/3/2011 X

4/10/2011 X X X X X X X X

4/17/2011 X X X X X X

4/24/2011 X X

5/1/2011 X X X X X X X

5/8/2011 X X X X X X X X

5/15/2011 X X X X X X

5/22/2011 X X X X

5/29/2011 X X X X X X

6/5/2011 X X X X X X X

6/12/2011 X X

6/19/2011 X X X X X

6/26/2011 X X X X X

7/3/2011 X X X X X X X

7/10/2011 X X X X X X X

7/17/2011 X X X X X X X

7/24/2011 X X X X X X
138

Table A14. Sample weeks that fish samples were collected at least once at seine sites in the 

Lower San Joaquin River Region during the 2010 field season.

Sample 

Week

Station Code

SJ083W SJ079E SJ077E SJ076W SJ074W SJ074A SJ068W SJ063W SJ058W SJ056E

8/2/2009

8/9/2009 X

8/16/2009

8/23/2009 X X X X

8/30/2009

9/6/2009 X X X X X

9/13/2009

9/20/2009 X X X

9/27/2009

10/4/2009 X X X X

10/11/2009

10/18/2009 X

10/25/2009

11/1/2009 X X

11/8/2009

11/15/2009 X X X

11/22/2009

11/29/2009 X X X X

12/6/2009

12/13/2009 X X X X

12/20/2009

12/27/2009 X X

1/3/2010 X X X

1/10/2010 X X X X

1/17/2010 X X

1/24/2010 X X

1/31/2010 X X X

2/7/2010 X X X

2/14/2010 X X

2/21/2010 X X

2/28/2010 X X

3/7/2010 X X X X

3/14/2010 X X X X X X

3/21/2010 X X

3/28/2010 X X

4/4/2010 X X

4/11/2010 X X

4/18/2010 X X X X

4/25/2010 X X

5/2/2010 X X X X

5/9/2010 X X

5/16/2010 X X

5/23/2010 X X X X X

5/30/2010 X X X X

6/6/2010 X X X

6/13/2010 X X X

6/20/2010 X X X

6/27/2010 X X X X

7/4/2010 X X X X X X X

7/11/2010

7/18/2010 X X X X

7/25/2010
139

Table A15. Sample weeks that fish samples were collected at least once at seine sites in the 

Lower San Joaquin River Region during the 2011 field season.

Sample 

Week

Station Code

SJ083W SJ079E SJ077E SJ076W SJ074W SJ074A SJ068W SJ063W SJ058W SJ056E

8/1/2010 X X X

8/8/2010

8/15/2010 X X X X

8/22/2010

8/29/2010

9/5/2010

9/12/2010 X

9/19/2010

9/26/2010 X X X X

10/3/2010

10/10/2010 X

10/17/2010

10/24/2010 X X X X

10/31/2010

11/7/2010 X X X

11/14/2010

11/21/2010 X X X X X

11/28/2010

12/5/2010 X X X X X

12/12/2010

12/19/2010

12/26/2010

1/2/2011 X X X

1/9/2011 X X

1/16/2011 X X

1/23/2011 X X

1/30/2011 X X X X

2/6/2011 X X X X

2/13/2011 X

2/20/2011 X

2/27/2011 X X X X

3/6/2011 X X

3/13/2011 X X X X

3/20/2011

3/27/2011

4/3/2011 X

4/10/2011 X

4/17/2011 X

4/24/2011 X

5/1/2011 X

5/8/2011 X

5/15/2011 X

5/22/2011 X

5/29/2011 X X X X

6/5/2011 X X X X X X X

6/12/2011 X X X X

6/19/2011 X X X X

6/26/2011 X X X

7/3/2011 X X X X X X

7/10/2011

7/17/2011 X X X X X

7/24/2011
140

Table A16. Sample weeks that fish samples were collected at least once at seine sites in 

the San Francisco/San Pablo Bays Region during the 2010 field season.

Sample 

Week

Station Code

SA009E SA007E SA001M SP003E SA010W SA008W SA004W SP001W SP000W

8/2/2009 X X X

8/9/2009 X X X X

8/16/2009 X X X

8/23/2009 X X X X

8/30/2009 X X

9/6/2009 X X X X

9/13/2009 X X X X

9/20/2009 X X X X

9/27/2009 X X X X X

10/4/2009 X X X

10/11/2009 X X X X X

10/18/2009 X X X X

10/25/2009 X X X X X

11/1/2009 X X X X

11/8/2009 X X X X X

11/15/2009 X X X X

11/22/2009 X X X X

11/29/2009 X X X X

12/6/2009 X X X X

12/13/2009 X X X X

12/20/2009 X X X X X

12/27/2009 X X X

1/3/2010 X X X X

1/10/2010 X X X

1/17/2010 X X X X X

1/24/2010 X X X X

1/31/2010 X X X X X

2/7/2010 X X X X

2/14/2010 X X X X

2/21/2010 X X X X

2/28/2010 X X X X X

3/7/2010 X X X X

3/14/2010 X X X X

3/21/2010 X X X X

3/28/2010 X X X X X

4/4/2010 X X X

4/11/2010 X X X X X

4/18/2010 X X X

4/25/2010 X X

5/2/2010 X X X

5/9/2010 X X

5/16/2010 X X X X

5/23/2010 X X X X X

5/30/2010 X X X X

6/6/2010 X X X X X

6/13/2010 X X

6/20/2010 X X X X X

6/27/2010 X X X X

7/4/2010 X X X X X

7/11/2010

7/18/2010 X X X X X

7/25/2010 X X X
141

Table A17. Sample weeks that fish samples were collected at least once at seine sites in 

the San Francisco/San Pablo Bays Region during the 2011 field season.

Sample 

Week

Station Code

SA009E SA007E SA001M SP003E SA010W SA008W SA004W SP001W SP000W

8/1/2010 X X X X

8/8/2010 X X X

8/15/2010 X X X X X

8/22/2010 X X X

8/29/2010 X X X X X

9/5/2010 X X X X

9/12/2010 X X X X X

9/19/2010 X X X X

9/26/2010 X X X X X

10/3/2010 X X X X

10/10/2010 X X X X

10/17/2010 X X X X

10/24/2010 X X X X X

10/31/2010 X X X X

11/7/2010 X X X X X

11/14/2010 X X X X

11/21/2010 X X X X X

11/28/2010 X X X

12/5/2010 X X X X X

12/12/2010 X X X X

12/19/2010 X X X

12/26/2010 X X X

1/2/2011 X X X X X X X X X

1/9/2011 X X X X X X X X

1/16/2011 X X X X X X X X

1/23/2011 X X X X X X

1/30/2011 X X X X X X X X

2/6/2011 X X X X X X X X

2/13/2011 X X X X X

2/20/2011 X X X X

2/27/2011 X X X X X

3/6/2011 X X X

3/13/2011 X X X X X

3/20/2011 X X X

3/27/2011 X X X X X

4/3/2011 X X X

4/10/2011 X X X X X

4/17/2011 X X X

4/24/2011 X X X

5/1/2011 X X

5/8/2011 X X X X X

5/15/2011 X X X

5/22/2011 X X

5/29/2011 X X X

6/5/2011 X X X

6/12/2011 X X X

6/19/2011 X X X X

6/26/2011 X X X X

7/3/2011 X X X X

7/10/2011 X X X X

7/17/2011 X X X

7/24/2011 X X X
Table A18. Total of individuals captured grouped by species, trawl site, and seine region during the 2010 field season. Fish species are 

listed in phylogenetic order. Seine regions represent sites as assigned in Table A1. 

Organism

Trawl Sites Beach Seine Regions

Sherwood 

Hbr.

Chipps 

Is. Mossdale 1 2 3 4 5 6 7

river lamprey, Lampetra ayresii 1 0 5 0 0 0 0 0 0 0

Pacific lamprey, Lampetra tridentata 3 0 361 0 0 0 0 0 0 0

lamprey unknown, Lampetra spp. 11 0 0 0 4 0 0 0 0 0

white sturgeon, Acipenser transmontanus 0 2 0 0 0 0 0 0 0 0

northern anchovy, Engraulis mordax 0 364 0 0 0 0 0 0 113 0

American shad, Alosa sapidissima 27 12618 12 0 63 16 19 1 2 1

Pacific herring, Clupea pallasii 0 132 0 0 0 0 0 0 1133 0

threadfin shad, Dorosoma petenense 161 373 1773 1275 203 255 2059 53 0 3

goldfish, Carassius auratus 3 0 30 1 1 0 0 1 0 0

red shiner, Cyprinella lutrensis 1 0 7 2121 33 0 544 16017 0 32

common carp, Cyprinus carpio 2 0 6 56 0 0 2 2 0 0

hitch, Lavinia exilicauda 0 0 0 33 4 12 7 1 0 0

hardhead, Mylopharodon conocephalus 0 0 0 64 9 1 0 0 0 0

golden shiner, Notemigonus crysoleucas 2 4 10 327 76 90 28 55 0 2

fathead minnow, Pimephales promelas 1 0 0 878 37 1 1 22 0 3

Sacramento splittail, Pogonichthys macrolepidotus 1 87 4021 1045 477 2124 1469 799 0 0

Sacramento pikeminnow, Ptychocheilus grandis 15 1 1 828 378 107 85 9 0 21

Sacramento sucker, Catostomus occidentalis 0 0 6 6137 2141 1559 253 142 0 65

white catfish, Ameiurus catus 0 3 178 0 2 0 0 1 0 0

black bullhead, Ameiurus melus 0 0 1 0 0 0 0 0 0 0

brown bullhead, Ameiurus nebulosus 0 0 1 0 0 0 0 0 0 0

channel catfish, Ictalurus punctatus 1 0 122 10 0 0 0 0 0 0

wakasagi, Hypomesus nipponensis 18 0 0 7 19 1 0 0 0 10

surf smelt, Hypomesus pretiosus 0 0 0 0 0 0 0 0 26 0

delta smelt, Hypomesus transpacificus 1 294 1 0 91 2 1 0 0 0

longfin smelt, Spirinchus thaleichthys 0 584 0 0 0 0 0 0 0 0
143

Table A18. Continued.

Organism

Trawl Sites Beach Seine Regions

Sherwood 

Hbr.

Chipps 

Is. Mossdale 1 2 3 4 5 6 7

steelhead, Oncorhynchus mykiss 40 119 3 10 14 2 0 0 0 0

 Unmarked steelhead 7 6 3 1 0 0 0 0 0 0

 Marked steelhead 33 113 0 9 14 2 0 0 0 0

Chinook salmon, Oncorhynchus tshawytscha 1224 5714 296 1127 2593 369 41 0 1 24

Unmarked winter-run 13 69 0 20 19 2 0 0 0 22

Unmarked fall-run 715 2430 296 997 2320 320 40 0 1 0

Unmarked spring-run 169 757 0 63 188 16 1 0 0 0

Unmarked late fall-run 3 11 0 9 29 4 0 0 0 0

Marked/CWT 324 2447 0 38 37 27 0 0 0 2

plainfin midshipman, Porichthys notatus 0 0 0 0 0 0 0 0 1 0

topsmelt, Atherinops affinis 0 50 0 0 0 0 0 0 4653 0

jacksmelt, Atherinopsis californiensis 0 64 0 0 0 0 0 0 2 0

inland silverside, Menidia beryllina 121 4 813 5269 15136 13623 15409 7107 97 1857

rainwater killifish, Lucania parva 0 0 0 0 17 39 72 1 29 0

western mosquitofish, Gambusia affinis 0 0 4 2127 247 173 148 1690 0 7

threespine stickleback, Gasterosteus aculeatus 3 12 0 0 138 32 0 0 48 0

bay pipefish, Syngathus leptorhynchus 0 0 0 0 0 0 0 0 233 0

brown rockfish, Sebastes auriculatus 0 0 0 0 0 0 0 0 8 0

prickly sculpin, Cottus asper 0 0 3 5 28 7 15 0 0 1

Pacific staghorn sculpin, Leptocottus armatus 0 1 0 0 21 31 1 0 519 0

tidepool sculpin, Oligocottus maculosus 0 0 0 0 0 0 0 0 2 0

cabezon, Scorpaenichthys marmortatus 0 0 0 0 0 0 0 0 2 0

striped bass, Morone saxatilis 5 896 127 5 15 6 4 24 3 0

green sunfish, Lepomis cyanellus 0 0 0 2 1 1 0 0 0 0

warmouth, Lepomis gulosus 5 0 0 0 0 1 0 0 0 0

bluegill, Lepomis macrochirus 14 3 534 98 58 71 99 290 0 2

redear sunfish, Lepomis microlophus 2 0 64 40 24 258 269 17 0 0
144

Table A18. Continued.

Organism

Trawl Sites Beach Seine Regions

Sherwood 

Hbr.

Chipps 

Is. Mossdale 1 2 3 4 5 6 7

smallmouth bass, Micropterus dolomieu 0 0 1 5 11 3 0 1 0 0

spotted bass, Micropterus punctulatus 0 1 1 13 41 22 2 3 0 1

largemouth bass, Micropterus salmoides 2 3 52 144 96 267 387 49 0 1

white crappie, Pomoxis annularis 0 1 15 41 4 0 0 0 0 0

black crappie, Pomoxis nigromaculatus 2 1 11 139 1 1 2 4 0 0

bigscale logperch, Percina macrolepida 0 0 5 722 28 14 12 5 0 1

barred surfperch, Amphistichus argenteus 0 0 0 0 0 0 0 0 8 0

shiner perch, Cymatogaster aggregata 0 0 0 0 0 0 0 0 64 0

black perch, Embiotoca jacksoni 0 0 0 0 0 0 0 0 2 0

walleye surfperch, Hyperprosopon argenteum 0 0 0 0 0 0 0 0 57 0

tule perch, Hysterocarpus traskii 1 15 1 90 202 197 3 0 0 0

dwarf surfperch, Micrometrus minimus 0 0 0 0 0 0 0 0 232 0

pile perch, Rhacochilus vacca 0 0 0 0 0 0 0 0 1 0

penpoint gunnel, Apodichthys flavidus 0 0 0 0 0 0 0 0 3 0

saddleback gunnel, Pholis ornata 0 0 0 0 0 0 0 0 10 0

crevice kelpfish, Gibbonsia montereyensis 0 0 0 0 0 0 0 0 27 0

yellowfin goby, Acanthogobius flavimanus 0 9 3 1 161 221 23 2 0 0

arrow goby, Clevelandia ios 0 0 0 0 0 0 0 0 321 0

longjaw mudsucker, Gillichthys mirabilis 0 0 0 0 0 0 0 0 1 0

cheekspot goby, Hypnus gilberti 0 0 0 0 0 0 0 0 4 0

bay goby, Lepidogobius lepidus 0 0 0 0 0 0 0 0 5 0

Shokihaze goby, Tridentiger barbatus 0 5 0 0 0 0 0 0 0 0

Shimofuri goby, Tridentiger bifasciatus 0 17 3 0 71 27 7 0 2 0

English sole, Parophrys vetulus 0 0 0 0 0 0 0 0 12 0

starry flounder, Platichthys stellatus 0 6 0 0 1 0 0 0 11 0

diamond turbot, Pleuronichthys guttulatus 0 0 0 0 0 0 0 0 17 0

sand sole, Psettichthys melanostictus 0 0 0 0 0 0 0 0 5 0

unidentified fish 0 0 1 0 0 0 0 0 0 0
145

Table A19. Total of individuals captured grouped by species, trawl site, and seine region during the 2011 field season. Fish species are 

listed in phylogenetic order. Seine regions represent sites as assigned in Table A1.

Organism

Trawl Sites Beach Seine Regions

Sherwood 

Hbr.

Chipps 

Is. Mossdale 1 2 3 4 5 6 7

river lamprey, Lampetra ayresii 1 0 0 0 0 0 0 0 0 0

Pacific lamprey, Lampetra tridentata 1 0 5 0 0 0 0 0 0 0

lamprey unknown, Lampetra spp. 0 0 0 1 1 0 0 0 0 0

leopard shark, Triakis semifasciata 0 0 0 0 0 0 0 0 1 0

thornback, Platyrhinoidis triseriata 0 0 0 0 0 0 0 0 1 0

white sturgeon, Acipenser transmontanus 0 0 0 0 0 0 0 0 0 0

northern anchovy, Engraulis mordax 0 425 0 0 0 0 0 0 21 0

American shad, Alosa sapidissima 36 5519 6 1 60 21 0 0 2 0

Pacific herring, Clupea pallasii 0 149 0 0 0 0 0 0 727 0

threadfin shad, Dorosoma petenense 75 408 1786 1042 447 32 4036 174 1 3

goldfish, Carassius auratus 3 0 159 8 0 1 0 21 0 0

red shiner, Cyprinella lutrensis 0 0 20 1367 40 6 1075 8599 0 16

common carp, Cyprinus carpio 20 0 356 113 146 61 31 441 0 0

hitch, Lavinia exilicauda 0 0 6 76 38 232 1 0 0 0

hardhead, Mylopharodon conocephalus 0 0 0 203 41 0 0 1 0 0

golden shiner, Notemigonus crysoleucas 4 5 20 2606 102 70 63 7 0 8

fathead minnow, Pimephales promelas 0 0 2 457 55 0 6 20 0 9

Sacramento blackfish, Orthodon microlepidotus 0 0 3 0 0 0 0 1 0 0

Sacramento splittail, Pogonichthys macrolepidotus 4 66 69585 4267 7488 19009 6413 8235 49 1

Sacramento pikeminnow, Ptychocheilus grandis 52 6 2 2122 2095 131 74 31 0 9

Sacramento sucker, Catostomus occidentalis 0 0 55 8037 4953 562 87 947 0 422

white catfish, Ameiurus catus 3 1 98 0 2 1 2 2 0 0

black bullhead, Ameiurus melus 0 0 2 1 4 0 1 0 0 0

brown bullhead, Ameiurus nebulosus 0 0 0 0 3 1 0 0 0 0

channel catfish, Ictalurus punctatus 1 0 97 3 0 0 0 0 0 0

wakasagi, Hypomesus nipponensis 4 3 0 1 29 0 0 0 0 0
146

Table A19. Continued.

Organism

Trawl Sites Beach Seine Regions

Sherwood 

Hbr.

Chipps 

Is. Mossdale 1 2 3 4 5 6 7

surf smelt, Hypomesus pretiosus 0 0 0 0 0 0 0 0 4 0

delta smelt, Hypomesus transpacificus 0 315 0 0 58 0 0 0 0 0

longfin smelt, Spirinchus thaleichthys 0 215 0 0 1 0 0 0 3 0

steelhead, Oncorhynchus mykiss 40 100 4 7 4 1 0 0 0 0

 Unmarked steelhead 2 8 3 0 3 0 0 0 0 0

 Marked steelhead 38 92 1 7 1 1 0 0 0 0

Chinook salmon, Oncorhynchus tshawytscha 2378 5542 3662 4006 4123 514 18 23 5 285

 Unmarked winter-run 20 64 0 108 60 1 0 0 0 27

 Unmarked fall-run 1734 3574 3235 3487 3414 412 16 21 4 220

 Unmarked spring-run 350 594 0 365 557 97 2 0 1 36

 Unmarked late fall-run 2 13 0 10 25 0 0 0 0 2

 Marked/CWT 272 1297 427 36 67 4 0 2 0 0

plainfin midshipman, Porichthys notatus 0 0 0 0 0 0 0 0 0 0

topsmelt, Atherinops affinis 0 137 0 0 0 0 0 0 4967 0

jacksmelt, Atherinopsis californiensis 0 0 0 0 0 0 0 0 3 0

inland silverside, Menidia beryllina 25 0 1178 6526 33168 16052 12684 3546 30 3874

rainwater killifish, Lucania parva 0 0 0 0 26 94 203 0 2 0

western mosquitofish, Gambusia affinis 0 0 2 1051 242 270 134 654 1 4

threespine stickleback, Gasterosteus aculeatus 0 3 0 0 17 4 0 0 185 2

bay pipefish, Syngathus leptorhynchus 0 0 0 0 0 0 0 0 316 0

prickly sculpin, Cottus asper 0 0 0 12 83 27 22 22 0 0

Pacific staghorn sculpin, Leptocottus armatus 0 0 0 0 21 10 0 0 623 0

tidepool sculpin, Oligocottus maculosus 0 0 0 0 0 0 0 0 2 0

cabezon, Scorpaenichthys marmortatus 0 0 0 0 0 0 0 0 1 0

striped bass, Morone saxatilis 3 308 55 3 114 0 88 9 11 0

green sunfish, Lepomis cyanellus 0 0 0 2 4 0 2 0 0 0

warmouth, Lepomis gulosus 0 0 0 1 0 1 1 0 0 0
147

Table A19. Continued.

Organism

Trawl Sites Beach Seine Regions

Sherwood 

Hbr.

Chipps 

Is. Mossdale 1 2 3 4 5 6 7

bluegill, Lepomis macrochirus 6 2 269 78 42 110 266 128 0 0

redear sunfish, Lepomis microlophus 4 0 69 42 62 422 767 19 0 0

redeye bass, Micropterus coosae 0 0 0 0 2 0 0 0 0 0

smallmouth bass, Micropterus dolomieu 0 0 2 2 16 1 2 1 0 0

spotted bass, Micropterus punctulatus 1 0 14 10 124 1248 9 6 0 0

largemouth bass, Micropterus salmoides 5 0 35 228 218 400 458 44 0 0

white crappie, Pomoxis annularis 0 0 19 28 3 0 0 1 0 0

black crappie, Pomoxis nigromaculatus 7 0 74 77 5 4 2 1 0 0

bass unknown, Micropterus spp. 0 0 1 0 0 0 0 0 0 0

bigscale logperch, Percina macrolepida 0 0 5 576 44 6 17 126 0 0

barred surfperch, Amphistichus argenteus 0 0 0 0 0 0 0 0 14 0

shiner perch, Cymatogaster aggregata 0 0 0 0 0 0 0 0 42 0

black perch, Embiotoca jacksoni 0 0 0 0 0 0 0 0 2 0

walleye surfperch, Hyperprosopon argenteum 0 0 0 0 0 0 0 0 105 0

tule perch, Hysterocarpus traskii 2 5 1 26 600 334 13 0 0 0

dwarf surfperch, Micrometrus minimus 0 0 0 0 0 0 0 0 260 0

white seaperch, Phanerodonfurcatus 0 0 0 0 0 0 0 0 1 0

pile perch, Rhacochilus vacca 0 0 0 0 0 0 0 0 1 0

penpoint gunnel, Apodichthys flavidus 0 0 0 0 0 0 0 0 2 0

saddleback gunnel, Pholis ornata 0 0 0 0 0 0 0 0 0 0

crevice kelpfish, Gibbonsia montereyensis 0 0 0 0 0 0 0 0 2 0

yellowfin goby, Acanthogobius flavimanus 0 1 3 2 97 24 11 1 54 0

arrow goby, Clevelandia ios 0 0 0 0 0 0 0 0 734 0

longjaw mudsucker, Gillichthys mirabilis 0 0 0 0 0 0 0 0 3 0

cheekspot goby, Hypnus gilberti 0 0 0 0 0 0 0 0 1 0

bay goby, Lepidogobius lepidus 0 0 0 0 0 0 0 0 3 0

Shokihaze goby, Tridentiger barbatus 0 0 0 0 0 0 1 0 0 0
148

Table A19. Continued.

Organism

Trawl Sites Beach Seine Regions

Sherwood 

Hbr.

Chipps 

Is. Mossdale 1 2 3 4 5 6 7

Shimofuri goby, Tridentiger bifasciatus 3 0 1 0 136 10 4 0 0 0

chameleon goby, Tridentiger trigonocephalus 0 0 0 0 0 0 0 0 1 0

English sole, Parophrys vetulus 0 0 0 0 0 0 0 0 110 0

starry flounder, Platichthys stellatus 0 3 0 0 1 0 0 0 53 0

diamond turbot, Pleuronichthys guttulatus 0 0 0 0 0 0 0 0 28 0

sand sole, Psettichthys melanostictus 0 0 0 0 0 0 0 0 0 0

unidentified fish 0 0 5427 0 0 0 0 0 0 0
149

Table A20. Water year types for the Sacramento and San 

Joaquin River basins from 1978 to 2011 (CDWR 2012b). 

Water year types were classified as wet (W), above normal 

(AN), below normal (BN), dry (D), and critically dry (C).

Water Year Water Year Type

Sacramento River San Joaquin River

1978 AN W

1979 BN AN

1980 AN W

1981 D D

1982 W W

1983 W W

1984 W AN

1985 D D

1986 W W

1987 D C

1988 C C

1989 D C

1990 C C

1991 C C

1992 C C

1993 AN W

1994 C C

1995 W W

1996 W W

1997 W W

1998 W W

1999 W AN

2000 AN AN

2001 D D

2002 D D

2003 AN BN

2004 BN D

2005 AN W

2006 W W

2007 D C

2008 C C

2009 D BN

2010 BN AN

2011 W W
150

Table A21. Mean maximum water temperatures (°C) by month and field season measured at Mallard Island (near the Chipps 

Island Trawl Site) from 1989 to 2011. 

Field 

Season Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul Average

1989 21.60 20.34 18.98 15.79 11.63 9.06 9.98 13.93 17.91 19.23 20.58 22.28 16.775

1990 21.68 20.38 19.57 16.13 11.58 9.66 10.37 13.96 17.75 19.61 20.95 22.28 16.993

1991 22.00 21.58 19.79 14.76 9.81 7.91 12.40 --- 15.15 16.79 19.41 --- 15.962

1992 21.03 20.70 19.56 15.12 10.11 8.98 11.43 15.54 17.78 20.23 20.59 22.26 16.944

1993 21.87 20.61 20.94 16.59 10.83 8.82 10.92 14.98 15.68 19.04 20.69 21.90 16.906

1994 22.00 20.69 18.52 14.73 10.39 9.66 11.14 14.84 17.32 18.63 20.78 20.99 16.641

1995 22.33 20.92 18.46 13.69 10.22 10.67 11.75 12.74 15.07 16.24 19.27 21.31 16.057

1996 22.40 20.45 19.10 --- 10.88 10.91 12.17 13.25 16.06 18.56 21.13 22.27 17.016

1997 22.43 20.52 18.07 14.47 11.47 10.10 11.73 12.50 --- 20.73 21.62 22.27 16.902

1998 22.35 22.32 18.10 16.48 10.35 9.78 10.53 13.50 15.09 17.12 18.93 22.53 16.422

1999 23.36 21.97 18.14 14.81 9.87 8.71 10.11 12.24 15.01 17.39 20.11 21.90 16.133

2000 21.40 20.14 19.33 15.95 11.27 10.51 12.02 13.47 16.62 18.97 21.55 21.72 16.912

2001 22.60 21.81 18.55 13.77 11.59 9.69 10.35 14.80 16.83 21.02 22.40 22.17 17.131

2002 21.89 20.59 19.23 16.43 10.67 10.43 11.13 13.39 16.72 18.29 20.98 22.11 16.821

2003 21.06 20.84 18.21 14.87 11.41 10.58 11.52 14.25 15.56 18.06 20.88 22.62 16.655

2004 21.90 21.20 18.96 14.61 10.93 9.41 10.93 15.09 16.62 19.64 20.94 21.86 16.841

2005 21.93 21.80 18.09 14.20 10.65 9.88 11.75 14.96 15.89 18.56 20.18 22.65 16.711

2006 21.55 19.91 18.28 15.19 11.26 10.76 11.27 11.39 14.08 19.40 21.65 23.52 16.522

2007 21.29 19.87 17.32 15.02 10.75 8.24 10.68 13.97 16.29 18.61 20.47 21.74 16.187

2008 21.49 20.83 17.59 15.57 10.66 8.40 9.65 13.67 15.64 18.58 20.40 21.44 16.160

2009 21.70 20.82 18.11 15.39 10.68 9.20 10.68 13.39 16.21 18.97 20.28 21.41 16.403

2010 21.22 21.56 17.73 14.59 9.97 9.39 11.55 13.45 15.35 17.17 20.44 20.71 16.095

2011 20.07 20.71 18.82 14.81 11.03 9.06 10.25 11.58 15.32 16.78 19.04 21.67 15.762
151

Table A22. Mean maximum water temperatures (°C) by month and field season measured at Freeport on the Sacramento River 

from the 2000 to 2011. 

Field 

Season Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul Average

2000 21.41 20.23 17.13 12.83 9.89 9.84 10.59 12.16 16.48 18.81 21.87 21.35 16.049

2001 --- --- --- --- --- 8.45 9.36 14.45 16.97 22.39 22.27 22.68 16.651

2002 22.69 21.52 18.95 14.60 9.60 9.52 10.18 12.34 16.39 18.72 21.68 22.03 16.519

2003 21.90 20.83 17.25 13.54 10.57 10.75 10.66 13.82 14.93 16.97 20.90 21.90 16.169

2004 21.45 21.10 20.08 12.00 11.23 9.94 10.93 14.47 16.70 21.11 22.68 22.82 17.042

2005 22.48 21.13 17.74 13.50 10.13 9.13 11.70 14.11 15.85 17.34 19.12 23.10 16.278

2006 22.87 19.85 17.00 13.88 10.74 10.32 10.64 10.82 12.97 17.11 20.60 23.03 15.821

2007 21.90 19.75 17.12 14.05 9.88 8.05 11.20 --- 20.93 21.68 22.89 22.48 17.266

2008 22.89 20.57 16.89 14.39 9.65 8.44 9.94 14.13 16.92 21.05 22.14 23.39 16.700

2009 24.20 22.29 18.62 15.15 9.91 9.84 10.88 13.82 16.50 18.96 21.72 22.10 16.999

2010 22.41 22.35 17.45 13.42 9.32 9.82 11.84 13.54 14.98 16.85 19.74 22.24 16.164

2011 21.92 20.29 17.78 13.65 11.68 10.19 10.24 10.98 13.83 15.27 18.11 20.64 15.383
152

Table A23. Mean maximum water temperatures (°C) by month and field season measured at Vernalis on the San Joaquin 

River from the 2000 to 2011. 

Field 

Season Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul Average

2000 24.34 22.59 18.52 13.48 10.57 11.31 12.83 14.08 17.72 19.40 25.73 25.31 17.989

2001 --- --- --- --- --- 9.84 11.76 17.24 17.90 21.89 24.96 26.77 18.623

2002 26.37 23.85 19.69 15.07 10.85 10.74 13.14 15.65 18.45 20.27 25.36 27.16 18.884

2003 26.32 24.10 18.56 14.22 11.21 12.05 13.05 14.67 16.93 20.56 22.92 27.29 18.490

2004 26.02 24.30 19.44 13.12 11.23 10.50 12.47 16.87 18.84 21.39 24.42 26.76 18.778

2005 26.47 23.50 18.56 13.23 10.42 9.82 12.82 14.32 14.50 16.73 19.32 23.45 16.928

2006 24.39 22.20 18.48 14.08 11.34 10.90 11.57 11.76 14.88 18.48 20.92 23.94 16.912

2007 22.60 20.35 16.14 14.07 10.41 --- 12.51 16.53 18.23 19.20 23.20 24.78 18.001

2008 26.15 23.04 17.90 14.23 9.65 8.81 12.91 15.46 16.87 19.34 24.95 26.46 17.981

2009 26.58 24.02 18.49 14.58 9.83 10.38 12.88 16.33 18.03 20.67 23.50 26.74 18.503

2010 26.07 23.09 17.25 13.35 10.17 10.88 13.36 15.26 16.32 16.59 20.51 24.53 17.282

2011 25.51 --- --- --- --- 10.48 10.80 12.76 16.08 16.77 18.34 20.85 16.450
153

Table A24. Recoveries of all coded wire tagged juvenile a) winter-, b) fall-, c) spring-, and d) late fall-run Chinook 

salmon by the DJFMP and fish facilities during the 2010 field season by release location and hatchery of origin. The 

hatcheries of origin included the Coleman National Fish Hatchery (ColemNFH), Livingston Stone National Fish 

Hatchery (LivinNFH), Feather River Fish Hatchery (FeathFH), Mokelumne River Fish Hatchery (MokFH), Nimbus 

Fish Hatchery (NimbFH), and Merced River Fish Facility (MercFF; PSMFC 2012).

Release Location

(Hatchery of Origin)

Recovery Location

Region 1Region 2Region 3Region 4Region 5Region 6Region 7

Chipps Island 

Trawl Site

Sacramento 

Trawl Site

Mossdale 

Trawl Site

DJFMP Total

Federal Fish 

Facility

State Fish 

Facility

a) Winter-run

Caldwell Park (LivinNFH) 5 0 0 0 0 0 0 54 22 0 81 23 6

b) Fall-run

American River (NimbFH) 0 7 2 0 0 0 0 245 4 0 258 4 0

Battle Creek (ColemNFH) 19 11 1 0 0 0 1 516 101 0 649 2 1

Jersey Point (MercFF) 0 0 0 0 0 0 0 19 0 0 19 0 0

San Pablo Bay (FeathFH) 0 0 0 0 0 0 0 6 0 0 6 0 0

Sherman Island (MokFH) 0 5 19 0 0 0 0 1285 0 0 1309 1 1

Wickland Oil (FeathFH) 0 0 0 0 0 0 0 3 0 0 3 0 0

c) Spring-run

Boyd’s Ramp (FeathFH) 2 4 0 0 0 0 0 188 180 0 374 0 0

San Pablo Bay (FeathFH) 0 0 0 0 0 0 0 3 0 0 3 0 0

d) Late fall-run

Battle Creek (ColemNFH) 11 6 2 0 0 0 1 66 4 0 90 185 128
154

Table A25. Recoveries of all coded wire tagged juvenile a) winter-, b) fall-, c) spring-, and d) late fall-run 

Chinook salmon by the DJFMP during the 2011 field season by release location and hatchery of origin. The 

hatcheries of origin included the Coleman National Fish Hatchery (ColemNFH), Livingston Stone National 

Fish Hatchery (LivinNFH), Feather River Fish Hatchery (FeathFH), Mokelumne River Fish Hatchery 

(MokFH), Nimbus Fish Hatchery (NimbFH), and Merced River Fish Facility (MercFF; PSMFC 2012).

Release Location

(Hatchery of Origin)

Recovery Location

Region 1Region 2Region 3Region 4Region 5Region 6Region 7

Chipps Island 

Trawl Site

Sacramento 

Trawl Site

Mossdale

Trawl Site

DJFMP Total

a) Winter-run

Caldwell Park (LivinNFH) 0 0 0 0 0 0 0 3 0 0 3

b) Fall-run

American River (NimbuFH) 0 37 0 0 0 0 0 82 1 0 120

Battle Creek (ColemNFH) 12 9 0 0 0 0 0 355 172 0 548

Discovery Park (NimbuFH) 0 5 0 0 0 0 0 229 47 0 281

Thermalito Bypass (Wild) 0 0 0 0 0 0 0 1 1 0 2

Wickland Oil (FeathFH) 0 0 0 0 0 0 0 2 0 0 2

Wickland Oil (NimbuFF) 0 0 0 0 0 0 0 3 0 0 3

Merced River (MercFF) 0 0 0 0 0 0 0 1 0 151 152

San Joaquin River (MercFF) 0 0 0 0 0 0 0 0 0 1 1

Mokelumne River (MokFH) 0 0 0 0 0 0 0 5 0 0 5

Mossdale (MercFF) 0 0 0 0 2 0 0 1 0 0 3

Hatfield State Park (MercFF) 0 0 0 0 0 0 0 0 0 192 192

San Pablo Bay (FeathFH) 0 0 0 0 0 0 0 4 0 0 4

Sherman Island (MokFH) 0 1 4 0 0 0 0 199 0 0 204

c) Spring-run

Boyds Pump (FeathFH) 22 7 0 0 0 0 0 278 34 0 341

d) Late fall-run

Battle Creek (ColemNFH) 1 8 0 0 0 0 0 106 8 0 123
155

Table A26. Total adult Chinook salmon escapement estimates by race 

for the Sacramento and San Joaquin River basins from 1978 to 2011 

(CDFG 2012).

Year Winter-run Fall-run Spring-run Late fall-run

1978 25,012 156,962 8,126 12,479

1979 2,364 227,646 3,116 10,284

1980 1,156 172,137 12,464 9,093

1981 22,797 260,259 22,105 6,718

1982 1,281 230,706 27,890 6,899

1983 1,831 205,290 7,958 15,089

1984 2,763 262,907 9,599 10,388

1985 5,407 356,304 15,221 10,180

1986 2,596 297,820 25,696 8,301

1987 2,185 301,583 13,888 16,571

1988 2,878 268,436 18,933 13,218

1989 696 182,350 12,163 12,872

1990 430 87,853 7,683 8,078

1991 211 132,455 5,926 8,263

1992 1,240 110,413 3,044 10,131

1993 387 165,423 6,076 1,267

1994 186 220,667 6,187 889

1995 1,297 330,168 15,238 489

1996 1,337 351,551 9,083 1,385

1997 880 402,797 5,193 4,578

1998 2,992 246,026 31,649 42,419

1999 3,288 414,259 10,100 15,758

2000 1,352 485,681 9,244 12,883

2001 8,224 624,631 17,598 21,813

2002 7,441 872,669 17,419 40,406

2003 8,218 590,992 17,691 8,772

2004 7,869 386,848 13,982 14,090

2005 15,839 437,693 16,126 16,188

2006 17,296 292,954 10,948 15,047

2007 2,542 97,168 9,935 18,773

2008* 2,830 71,870 6,420 10,317

2009* 4,537 53,129 3,801 9,982

2010* 1,596 163,190 3,792 9,895

2011* 827 227,889 5,033 8,418

* indicates years containing preliminary data