U.S. Fish and Wildlife Service

Annual Report:

Juvenile fish monitoring during the 2012 and 2013 field seasons within the San 

Francisco Estuary, California

Denise Barnard, Jonathan Speegle, and Joseph Kirsch*

U.S. Fish and Wildlife Service

Lodi Fish and Wildlife Office

Delta Juvenile Fish Monitoring Program

850 South Guild Ave, Suite 105

Lodi, CA 95240

(209) 334-2968

August 2015

*Corresponding author: joseph_kirsch@fws.gov
ii

EXECUTIVE SUMMARY

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

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

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

sites have been sampled weekly or biweekly within the Estuary and lower Sacramento and San 

Joaquin rivers. The objectives of the DJFMP Annual Report for the 2012 (August 1, 2011 to July 

31, 2012) and 2013 (August 1, 2012 to July 31, 2013) field seasons were to (1) report water 

quality information collected concurrently while monitoring fish during the 2012 and 2013 field 

seasons, (2) document the fish assemblage structure at monitoring sites, (3) determine the 

abundance and distribution of naturally and hatchery produced juvenile Chinook Salmon 

migrating into and out of the Delta, (4) document the length frequency distributions of unmarked 

juvenile Chinook Salmon captured, and (5) discuss how the relative abundance indices of 

unmarked winter-run sized or older juvenile Chinook Salmon occurring near Sacramento 

informed real-time Delta Cross Channel (DCC) water operation decisions.

We generally observed highly variable water quality parameters across all trawl sites and seine 

regions. We observed overall higher water temperatures in 2013 than in 2012, frequently 

exceeding 25°C in the summer months. We also observed highly variable dissolved oxygen 

values in the lower San Joaquin River during the 2013 field season, which increased to above 12 

mg/L in May and decreased to less than 3 mg/L during June and July. In general, the turbidity 

was lower within the Central Delta and South Delta seine regions relative to other regions 

throughout most of the field seasons. Little distinct inter-annual patterns were observed in water 

conductivity in trawl sites or seine regions. 

The fish assemblage was dominated by nonnative resident fish, and there was an overall increase 

of nonnative fish captured during the 2013 field season compared to 2012. In general, 

anadromous-pelagic-nonnative species dominated at Chipps Island and resident pelagicnonnative fish dominated at the Mossdale Trawl Site. In contrast, anadromous-pelagic-native 

fish were relatively more abundant at the Sacramento Trawl Site. The mean yearly catch-per-unit 

effort estimates among beach seine regions demonstrated that fish densities for most assemblage 

groups were relatively low during the 2012 field season and increased slightly in 2013.

We developed a technique to estimate the origin of unmarked juvenile Chinook Salmon using the 

known ratio of unmarked to marked individuals in hatchery release groups, and estimated that 

nearly all juvenile salmon captured using beach seines since the 2000 field season were of 

natural origin. Conversely, most of the hatchery origin fish were captured using trawls. This 

suggested that hatchery juvenile Chinook Salmon may be less likely to occur in unobstructed 

near shore habitats within the San Francisco Estuary than natural origin juvenile Chinook 

Salmon.

We also estimated that the number of juvenile Chinook Salmon migrating into the Delta 

increased in the 2013 field season relative to 2012. However, the overall number of juvenile 

Chinook Salmon migrating out of the Delta decreased in the 2013 field season relative to 2012. 

We also observed that the overall abundance of winter-run and fall-, late fall-, and spring-run 
iii

sized juvenile Chinook Salmon migrating out of the Delta in the 2012 and 2013 field seasons has 

decreased relative to historic densities. 

The DJFMP calculated a Sacramento Catch Index (SCI) using the relative abundance indices of 

unmarked winter-run or older juvenile Chinook Salmon near Sacramento. The SCI did not 

trigger any DCC operations in the 2012 field season. However, the SCI exceeded the threshold 

of the salmon decision process on 13 sampling dates during the 2013 field season. This, in 

conjunction with other criteria, either triggered or maintained the closure of the DCC gates on 12 

occasions.

The suggested citation for this report is:

Barnard, D., J. Speegle, and J. Kirsch. 2015. Annual report: juvenile fish monitoring during the 

2012 and 2013 field seasons within the San Francisco Estuary, California. Lodi Fish and Wildlife 

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

TABLE OF CONTENTS

Executive Summary........................................................................................................................ ii

Acknowledgments........................................................................................................................... v

Acronyms....................................................................................................................................... vi

Long-Term Monitoring................................................................................................................... 7

Introduction ................................................................................................................................. 7

Methods....................................................................................................................................... 8

Monitoring Locations.............................................................................................................. 8

Trawl Methodology ............................................................................................................... 10

Beach Seine Methodology..................................................................................................... 15

Fish Processing...................................................................................................................... 17

Water Quality ........................................................................................................................ 18

Fish Assemblage.................................................................................................................... 19

Estimate of Hatchery and Natural Origin Juvenile Chinook Salmon.................................... 19

Relative Abundance Calculations.......................................................................................... 21

Absolute Abundance Calculation .......................................................................................... 23

Length Frequency.................................................................................................................. 25

River Flow Conditions........................................................................................................... 25

Results and Discussion.............................................................................................................. 26

Water Quality ........................................................................................................................ 27

Fish Assemblage.................................................................................................................... 37

Juvenile Chinook Salmon...................................................................................................... 44

Monitoring for Delta Cross Channel Operations.......................................................................... 72

Introduction ............................................................................................................................... 72

Methods..................................................................................................................................... 73

Results and Discussion.............................................................................................................. 76

References..................................................................................................................................... 79

Appendix....................................................................................................................................... 84
v

ACKNOWLEDGMENTS

All fish sampling presented in this report was conducted for the Interagency Ecological Program

(IEP) for the San Francisco Estuary and funded by the California Department of Water 

Resources and the U.S. Bureau of Reclamation. Members of the IEP include three state agencies 

(the California Department of Water Resources, California Department of Fish and Wildlife, and 

State Water Resources Control Board) and six federal agencies (the U.S. Bureau of Reclamation, 

U.S. Geological Survey, U.S. Fish and Wildlife Service, National Marine Fisheries Service, 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 weather conditions to collect these data. We 

would like to especially thank Amber Aguilera, Crystal Castle, Laura Chumney, Jeffrey Cullen, 

Lauren Damon, Dustin Dinh, David Dominguez, Kate Erly, Kyle Fronte, Garrett Giannetta, 

Christopher Hart, Jack Ingram, Carlie Jackson, David LaPlante, Jerrica Lewis, Mike Marshall, 

Tim Matt, Paul Miklos, Greg Nelson, Jacob Osborne, John Pedretti, Scott Porter, Pam Tarelli, 

Phil Voong, and Jolene Willis for biological sampling; Jackie Hagen, Curtis Hagen, Ron Hagins, 

Patrick Hapgood, and Bill Powell for boat operation; and Angie Bourandas for helping oversee 

data entry and quality control during the 2012 and 2013 field seasons. We would also like to 

thank Patricia Brandes, Matthew Dekar, Lori Smith, and Kim Webb for improvements to earlier 

drafts of this report. 

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

ACRONYMS

The following acronyms have been used in this report:

CI—Confidence interval

CDFW—California Department of Fish and Wildlife

CDWR—California Department of Water Resources

CPUE—Catch-per-unit effort

CVP—Central Valley Project

CWT—Coded wire tag

DAT—Data Assessment Team

DCC—Delta Cross Channel

DJFMP—Delta Juvenile Fish Monitoring Program

DOSS—Delta Operations for Salmon and Sturgeon working group

ESA—Endangered Species Act

FL—Fork length

IEP—Interagency Ecological Program

KDTR—Kodiak trawl

KLCI—Knights Landing Catch Index

LDC—Length-at-capture-date criteria

LFWO—Lodi Fish and Wildlife Office

MWTR—Mid-water trawl

NMFS—National Marine Fisheries Service

PSMFC—Pacific States Marine Fisheries Commission

RM—River mile

RMIS—Regional Mark Information System

SCI—Sacramento Catch Index

SD—Standard deviation

SE—Standard error

SJRGA—San Joaquin River Group Authority

SWP—State Water Project

SWRCB—State Water Resources Control Board

USBR—United States Bureau of Reclamation

USFWS—United States Fish and Wildlife Service

USGS—United States Geological Survey

WOMT—Water Operations Management Team
7

LONG-TERM MONITORING

Introduction

The San Francisco Estuary (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, 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 Estuary and its watershed. The damming 

of most rivers, confinement of channels, and water diversions and exports has subjected the 

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

organisms (Stevens and Miller 1983; Nichols et al. 1986; 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 monitored and studied, in part, by the Delta 

Juvenile Fish Monitoring Program (DJFMP) of the Lodi Fish and Wildlife Office (LFWO,

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

operations on fish populations.

The DJFMP, as part of the Interagency Ecological Program, has been monitoring populations of 

juvenile Chinook Salmon Oncorhynchus tshawytscha within the Sacramento-San Joaquin Delta 

(Delta) and its watershed since 1976 (Dekar et al. 2013). The DJFMP and its goals have evolved 

based on water management needs and endangered species listings. Prior to 1992, the DJFMP 

conducted annual monitoring between April and June to assess the effects of water operations on 

the inter- and intra-annual abundance and distribution of primarily juvenile fall-run Chinook 

Salmon within the Delta and lower Sacramento River. Following the listing of Sacramento River 

winter-run Chinook Salmon as endangered by the State of California in 1989 (CDFW 2005) and 

by the National Marine Fisheries Service in 1994 (59 FR 440), the DJFMP expanded the longterm sampling program to one that operated between October and June to collect more 

information on all races of juvenile Chinook Salmon in the Estuary. The DJFMP was further 

expanded in 1995 to sample year-round, in part, to expand the temporal and geographic 

monitoring of resident fish and Central Valley Steelhead Oncorhynchus mykiss (Dekar et al. 

2013). Today, year-round monitoring continues with an emphasis on populations of all races of 

Chinook Salmon in the Delta per the monitoring and reporting terms of the Biological Opinion 

and Conference Opinion on the Long-Term Operations of the Central Valley Project (CVP) and 

State Water Project (SWP, NMFS 2009a).

In general, the fish data collected by the DJFMP are intended to provide basic biological and 

demographic information that can be used to assess trends over time. The first section of this 

report will focus on the DJFMP’s long-term observations of juvenile Chinook Salmon and fish 

assemblage structure. The objectives of the annual report for the 2012 (August 1, 2011 to July 

31, 2012) and 2013 (August 1, 2012 to July 31, 2013) field seasons were to (1) report water 

quality information collected concurrently while monitoring fish during the 2012 and 2013 field

seasons, (2) document the fish assemblage structure at monitoring sites, (3) determine the 

abundance and distribution of naturally and hatchery produced juvenile Chinook Salmon 
8

migrating into and out of the Delta, and (4) document the length frequency distributions of 

unmarked juvenile Chinook Salmon. Although the water quality data are intended to document 

the spatial and temporal variation of potential fish habitat characteristics within the Estuary and 

lower rivers, rigorous fish-habitat analyses are beyond the scope of this report.

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 2012 and 2013 field 

seasons, the DJFMP sampled fishes at 3 trawl sites and 58 beach seine 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 A.1).

We used surface trawls to examine the relative abundance of fishes migrating into and out of the 

Delta. Trawl sites were located at the entry (Sacramento and Mossdale trawl sites) and exit 

(Chipps Island Trawl Site) points of the Delta (Figure 1; Table A.1). In general, the DJFMP 

sampled each trawl site three days per week, with ten tows per day throughout the 2012 and 2013 

field seasons. Trawl sites were generally sampled Monday, Wednesday, and Friday each week 

throughout the field season to maximize temporal coverage. The California Department of Fish 

and Wildlife (CDFW) has traditionally sampled the Mossdale Trawl Site, following similar 

methodologies, in place of the DJFMP between April and June (SJRGA 2009). Data collected 

from both the DJFMP and CDFW at the Mossdale Trawl Site are included in this report.

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

shallow near-shore habitats (e.g., beaches and boat ramps ≤ 1.2 m in depth) throughout the lower 

Sacramento and San Joaquin rivers and the Estuary. Beach seine sites were stratified into six

geographic seine regions: (1) Lower Sacramento River, (2) North Delta, (3) Central Delta, (4) 

South Delta, (5) Lower San Joaquin River, and (6) San Francisco and San Pablo Bay (Figure 1; 

Table A.1). Seine regions were delineated by proximity to canals or water bypasses where fish 

may be diverted from historical migration routes. 

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

sampling or make it necessary to temporarily relocate seine sites (e.g., tidal conditions, or 

submerged or floating aquatic vegetation blocking access to sites). If new seine sites were 

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

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

Accessibility of beach seine sites in the San Joaquin River Seine Region varied in difficulty 

between flow conditions. During the 2000–2012 field seasons, when the discharge of the lower 

San Joaquin River dropped below 51 m3/s boat access to specific beach seine locations became 

difficult, so only sites that were accessible from land were sampled (Table A.1). To 

accommodate for the inaccessible sites we sampled alternative sites, some of which were over 

100 m from the original sampling locations. However, we discontinued the use of alternative 

sites in the San Joaquin River Seine Region in the 2013 field season in order to decrease biases 

in fish abundance and distribution patterns caused by changing sites during variable flow 
9

conditions; and only the sites that were sampled when the river was above 51 m3/s during the 

2000–2012 field seasons were sampled throughout the entire 2013 field season. More 

information on monitoring site modifications can be found in the LFWO Metadata file at 

http://www.fws.gov/lodi/jfmp/.

Figure 1. Sites sampled during the 2012 and 2013 field season within the lower Sacramento and 

San Joaquin rivers and San Francisco Estuary.
10

In general, we sampled fishes at the beach seine sites one day per week, one time per day 

throughout the 2012 and 2013 field seasons within all seine regions except the Lower San 

Joaquin River and the San Francisco and San Pablo Bay seine regions. The beach seine sites that 

were located within the Lower San Joaquin River Seine Region were generally sampled one day 

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

1 to December 31. The beach seine sites that were located within the San Francisco and San 

Pablo Bay Seine Region were generally sampled one day per every two weeks, one time per day 

throughout the 2012 and 2013 field seasons based on logistical limitations and the low 

occurrence of fish species of management concern. 

Trawl Methodology

We sampled at trawl sites using 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 DJFMP exclusively used a MWTR at the Sacramento Trawl Site prior to 1994, and has 

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

thereafter (Dekar et al. 2013). The KDTR has been used in place of the MWTR at the 

Sacramento Trawl Site from October to March to maximize the capture of larger Chinook 

Salmon and to provide more robust juvenile winter-run Chinook Salmon catch indices (Dekar et 

al. 2013). 

During each sampling day, we attempted ten 20-minute tows between sunrise and sunset at all 

trawl sites. All tows were conducted mid-channel and facing upstream at the Sacramento and 

Mossdale trawl sites, which constitute a reach length of approximately 6.5 km and 3 km, 

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

in the north, south, and middle portions of the channel at the Chipps Island Trawl Site based on 

tidal influence on net water velocities. The Chipps Island Trawl Site 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 that the net mouth remained fully extended and submerged. The measure 

of the distance traveled during each tow was recorded using a calibrated mechanical flow meter 

(General Oceanics, Model #2030) deployed alongside the boat. 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 2). 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 by 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 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 
11

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

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

MWTR net used at the Sacramento Trawl Site (Figure 3). 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 

by 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. 

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 4A). 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 by 36 cm tall by 49 cm long) was composed of 0.18 cm thick aluminum 

that was perforated with 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 by 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. Additionally, at the front of each wing of the net 

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

while sampling. The KDTR nets were towed behind two boats sitting approximately 4.5 m apart 

(Figure 4B). 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), which was attached to the metal bar

on each side of the net. The net was fished approximately 31 m behind the boats. 

At the end of each MWTR tow, the net was retrieved by the towing vessel using winches to 

collect all the fishes observed in the cod ends. At the end of each KDTR tow, the two towing 

vessels (i.e., net and chase boats) would maneuver alongside each other, and the chase boat 

would transfer its tow rope to the net boat. Subsequently, the crew on the chase boat would travel 

downstream to the live box connected to the KDTR, retrieve, secure, and pull the live box from 

the water into the boat (Figure 5). All fishes collected from the cod end or live box were placed 

in a holding container filled with river water for processing. Lastly, the crew would determine 

the condition of each tow as either “normal” (defined as no twists, snags, or tears in the net, little 

to no [<5%] debris in/on the net, and no [<5%] blockage between the mouth of the net to the live 

box), “fair” (defined as partial twists, snags, or small tears in the net, some [5–25% coverage] 

debris in/on the net, or partial [5–25%] blockage between the mouth of the net to the live box), or

“poor” (defined as complete twists, snags, or large tears in the net, heavy [>25% coverage] 

debris in/on the net, or near complete [>25%] blockage between the mouth of the net to the live 

box).
12

Figure 2. Schematic drawing of the (A) mid-water trawl net and (B) hydrofoils and depressors 

used at the Sacramento Trawl Site during the 2012 and 2013 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 x 15.2 cm 

float secured with

stainless bolts

15.2 cm

Hydrofoil—top view Hydrofoil—side view

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

30.5 m 

bridle ropes

(A)

(B)
13

Figure 3. Schematic drawing of the (A) mid-water trawl net and (B) hydrofoils and depressors 

used at the Chipps Island Trawl Site during the 2012 and 2013 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 

float secured with 

stainless bolts

22.9 cm

Hydrofoil—top view Hydrofoil—side view

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

(A)

(B)

30.5 m 

bridle ropes
14

Figure 4. Schematic drawing of the (A) Kodiak trawl net used and (B) position of the boats 

during Kodiak trawling at the Sacramento and Mossdale trawl sites during the 2012 and 2013 

field seasons. 

Figure 5. The Kodiak trawl (A) live box (B) being retrieved, (C) 

secured, and (D) pulled into the vessel.

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 metal bar

Float line

Lead line

Float 

2.3 m bridle 

ropes 

30.5 m 

tow rope

(A)

(A) (B)

(C) (D)

(B) Top of metal bars

Tow rope Net

4.5 m
15

Beach Seine Methodology 

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

15.2 by 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. Occasionally rollers were added to the 

lead line of the beach seine to prevent the net from sinking into fine substrates (i.e., substrata 

with particles <62.5 μm in diameter), which would otherwise impede the completion of the seine 

haul. 

The beach seines were generally deployed by two crewmembers starting from the downstream 

portion of each site to limit disturbance (e.g., displacement of sediment into the site). Crew 

member 1 pulled the seine into the water, perpendicular from the shoreline, as crew member 2 

secured the opposite end of the seine to the shoreline (Figure 6A). After reaching a depth of up to 

1.2 m, a distance of up to 15 m, or an obstacle; crew member 1 stopped and measured the 

distance (i.e., length) to the shoreline and depth to the nearest 1 m and 0.1 m, respectively 

(Figure 7). Obstacles were defined as any structure that could compromise safety or gear 

efficiency; e.g., steep banks or holes, fast water current, submerged aquatic vegetation, or large 

woody debris. If the depths of the seine varied between measurements, the maximum seine depth 

was obtained by averaging the two depth measurements. Next, crew member 2 carried their end 

of the seine to crew member 1 and placed it 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 6B). Lastly, crew members 1 and 2 pulled the ends of the seine simultaneously 

toward and perpendicular to the shoreline while attempting to maintain the starting width (Figure 

6C). The net was continuously pulled towards the shoreline until the lead line of the seine bag 

was on shore (Figure 6D). 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. The crew would then determine the condition of the sample as either “normal”

(defined as no twists, snags, or tears in the net, and the seine was pulled steadily while keeping 

the lead line in contact with the substrate and float line at or above the water’s surface), “fair”

(defined as partial twists, snags, or small tears in the net, but the seine was pulled steadily while 

keeping the lead line in contact with the substrate and float line at or above the water surface), or 

“poor” (defined as complete twists, snags, or large tears in the net, or the seine was not pulled 

steadily, or the lead line was not in contact with the substrate, or float line was below the water

surface).
16

Figure 6. 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 7. Schematic diagram of beach seine measurements: (A) three-dimensional view and (B) 

overhead view.

(A)

(C) (D)

(B)

Length

Width

Shore

Depth 1 Depth 2

(B)

Width

Shore

Depth 1

Depth 2

Length

(A)
17

Fish Processing

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

the exception of five species that were readily identified at ≥ 20 mm FL: Sacramento Splittail 

Pogonichthys macrolepidotus, Three-spine Stickleback Gasterosteus aculeatus, Western 

Mosquito Fish Gambusia affinis, Rainwater Killifish Lucania parva, and Sacramento Sucker 

Catostomus occidentalis. 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, as designated by the river 

length-at-capture-date criteria (LDC, see paragraph below), or other species listed under the 

Endangered Species Act (ESA) were captured, a subsample of 50 individuals was randomly 

measured for FL and the rest were counted and not measured. If greater than 30 individuals of a 

non-listed species were captured, a subsample of 30 individuals was randomly measured for FL

and the rest were counted and not measured. Fish that could not be accurately identified in the 

field were preserved and brought back to the laboratory. The identification of preserved fishes 

was then confirmed with the use of dichotomous keys or with the aid of a microscope.

Only juvenile Chinook Salmon with missing (clipped) adipose fins were considered marked fish. 

In general, fish possessing other forms of marks (e.g., stain dye, disc tags, acoustic tags) were not 

included within this report to further minimize the influence of recaptures and/or unnatural 

occupancy induced by other fishery investigations. Stain dye marked juvenile Chinook Salmon 

released near the Mossdale Trawl Site were only used to estimate trawl efficiency (see “Absolute 

Abundance Calculation” section). All clipped juvenile Chinook Salmon observed during the 

2012 and 2013 field seasons were considered hatchery-reared and were brought back to the lab 

to process the coded wire tag (CWT).

Recovered CWTs can provide important biological information to natural resource managers 

(e.g., an individual's race, hatchery of origin, and the date and location released). Therefore, all 

clipped Chinook Salmon were euthanized in the field and brought back to the laboratory. We 

then removed, read, and recorded the tag code of all CWTs recovered. We obtained 

corresponding tag information (e.g., race and release location) from the Regional Mark 

Information System (RMIS) maintained by the Pacific States Marine Fisheries Commission 

(PSMFC 2014). Details regarding CWT recoveries during the 2012 and 2013 field seasons can 

be found in the “Appendix” section. 

The race of all unmarked juvenile Chinook Salmon was determined using the river LDC 

developed by Fisher (1992) and modified by Greene (1992). The assumptions associated with the 

river LDC for the Sacramento-San Joaquin River basin include that (1) spawning of fall-run 

Chinook Salmon occurs between October 1–December 31, (2) spawning of late fall-run Chinook 

Salmon occurs between January 1–April 15, (3) spawning of winter-run Chinook Salmon occurs 

between April 16–August 15, (4) spawning of spring-run Chinook Salmon occurs between 

August 16–September 30, 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 LDC 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 
18

spring-run due to the loss of headwater habitats (e.g., resulting from 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 river LDC

may actually be fall-run. Additionally, some genetic analyses of DNA genotypes have 

demonstrated the inaccuracy of the river LDC that has been used to determine Chinook Salmon 

races within the San Francisco Estuary, especially between fall- and spring-run salmon (e.g., 

Banks et al. 2000; Greig et al. 2003; Banks 2014). Therefore, we used the river LDC to 

differentiate only between winter-run and a combined group of fall-, late fall-, and spring-run 

juvenile Chinook Salmon. The race designations used in this report should be considered a rough 

approximation and not interpreted as definitive.

All juvenile Chinook Salmon collected at the Mossdale Trawl Site and within the Lower San 

Joaquin River Seine Region were classified as fall-run regardless of their length at the date of 

capture, and thus included in the fall-, late fall-, and spring-run group, 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). Although the South and Central Delta seine regions are 

located within the San Joaquin River basin, there is potential for late fall-, winter-, and springrun juveniles of Sacramento River origin to migrate into the interior delta through the Georgiana 

Slough, the Delta Cross Channel (DCC), and the San Joaquin River during water diversions or 

transfers. Therefore, the river LDC was still used to determine the race of juvenile Chinook 

Salmon within the South and Central Delta seine regions. 

Water Quality

We measured temperature, dissolved oxygen, turbidity, and conductivity immediately before 

each trawl and during or after each seine haul during the 2012 and 2013 field seasons. We have 

consistently measured water temperature at all monitoring sites during or immediately before 

each sampling occasion since the late 1970s. Additionally, we have consistently measured 

dissolved oxygen, turbidity, and conductivity at all monitoring locations since January of 2012. 

However, CDFW only measured water temperature at the Mossdale Trawl Site during April, 

May, and June of 2012 due to lack of the appropriate equipment. 

We used a YSI 85 or YSI PRO 2030 meter to measure water temperature to the nearest 0.1 ̊C, 

dissolved oxygen to the nearest 0.01 mg/L, and conductivity to the nearest 0.01 

microsiemen/centimeter (μS/cm) for freshwater or millisiemen/centimeter (mS/cm) for salt 

water. Turbidity was measured using a HACH 2100Q turbidity meter to the nearest 0.01 

nephelometric turbidity unit (NTU). All measurements or samples were collected 20–30 cm 

below the surface of the water 

We presented the raw temperature, dissolved oxygen, turbidity, and conductivity estimates by 

month for each trawl site and beach seine region during the 2012 and 2013 field seasons as box 

plots (median and percentiles) to demonstrate the spatial and temporal variability of the habitat 

conditions representative of our monitoring sites during sampling.
19

Fish Assemblage

We classified fish species into seven distinct assemblage groups based on shared origin, habitat 

requirements, and life history strategies (Moyle 2002): (1) anadromous-benthic-native, (2) 

anadromous-pelagic-native, (3) anadromous-pelagic-nonnative, (4) benthic-native, (5) benthicnonnative, (6) pelagic-native, and (7) pelagic-nonnative (Table A.2). All juvenile unmarked 

Chinook Salmon captured were considered members of the anadromous-pelagic-native group. 

No marked Chinook Salmon or steelhead were included in any of the assemblage groups, though 

unmarked hatchery Chinook Salmon were included. 

Estimate of Hatchery and Natural Origin Juvenile Chinook Salmon

In general, hatcheries have used CWTs, indicated by clipped adipose fins, to mark all hatchery 

produced late fall-, winter-, and spring-run juvenile Chinook Salmon in the Central Valley

(Kevin Niemela, USFWS, personal communication; Williams 2006). However, a small 

proportion of late fall-, winter-, and spring-run Chinook Salmon fin clips are missed during 

tagging at the hatchery, and recorded in RMIS as unmarked (Kevin Niemela, USFWS, personal 

communication; PSMFC 2014). Conversely, the marking and CWT tagging rates of hatchery 

reared 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 hatchery produced juvenile fall-run Chinook Salmon, where at least 25% of individuals within 

each hatchery release group are marked and have a CWT inserted (Nandor et al. 2010). Because 

unmarked hatchery reared juvenile Chinook Salmon are still being released into the Central 

Valley, there is considerable uncertainty concerning the origin (i.e., naturally or hatchery

produced) of unmarked juvenile Chinook Salmon observed during DJFMP monitoring. This 

uncertainty impacts the program’s ability to inform research or management decisions 

concerning naturally-produced juvenile Chinook Salmon (Williams 2006; Dekar et al. 2013).

Therefore, we developed an equation to estimate the origin of juvenile Chinook Salmon observed 

during the 2000 to 2013 field seasons. We applied the equation to all races of juvenile Chinook 

Salmon to account for any possible unmarked proportion of a hatchery release group, either

caused by intentional unmarking (fall-run), or clip failure during tagging (late fall-, winter-, and 

spring-run).We estimated the number of unmarked hatchery origin juvenile Chinook Salmon 

(Hs) for each sample (e.g., trawl tow or seine haul) and race group as: 

Hs = ∑(Cg x Pg) ( 1 )

where s indexes an individual sample (i.e., a beach seine haul or trawl tow), g indexes a CWT 

release groups, Cg represents the total number of marked individuals collected from the CWT 

release group, and Pg represents the proportion of unmarked to marked individuals within the 

CWT release group. Pg was obtained from state and federal hatchery records (PSMFC 2014). 

The primary assumption of this approach was that marked and unmarked individuals within a 

CWT release group have identical capture probabilities and availability during sampling.

We included juvenile Chinook Salmon that were reported as fall- and spring-run hybrids in 

hatchery records in the combined fall-, late fall-, and spring-run group. We also included all 
20

other hybrid-run juvenile Chinook Salmon without race descriptions in this group based on 

unlikely hybridization between winter-run Chinook Salmon and other races (Slater 1963). 

Additionally, we omitted any CWT release groups that were associated with “wild type” origin 

juvenile Chinook Salmon based on these groups being experimental and rare. 

We then summed the total number of unmarked hatchery origin juvenile Chinook Salmon 

observed within a sample day for each race group and monitoring site (Hd). Subsequently, we 

estimated the number of natural juvenile Chinook Salmon for each race group and monitoring 

site within a sample day (Wd) as:

Wd = Od − Hd( 2 )

where Od denotes the total number of unmarked juvenile salmon observed during a sample day 

for a race group and monitoring site. If the estimated number of unmarked hatchery origin 

individuals exceeded the total number of unmarked juvenile Chinook Salmon observed for a race 

group during a sample day at a monitoring location (occurred in < 1% of samples), we 

designated all unmarked individuals observed as unmarked hatchery individuals. All clipped 

juvenile Chinook Salmon included in the analysis were considered to be of hatchery origin.

Prior to 2000, large groups of unmarked fall-run juvenile Chinook Salmon were regularly 

released by the state and federal hatcheries throughout the Delta that were not associated with 

any marked group (Kevin Niemela, USFWS, personal communication; PSMFC 2014). 

Consequently, our approach to estimate the number of natural and hatchery juvenile Chinook 

Salmon at our monitoring locations could not be applied to our catch data for the fall-, late fall-, 

and spring-run group during this time. As a result, all unmarked fall-, late fall-, and spring-run

fish observed prior to the 2000 field season were considered to have an unknown origin. After 

2000, groups containing only unmarked individuals were released at Battle Creek, Sacramento 

River, Feather River, and downstream of Chipps Island. We assumed that unmarked releases 

downstream of Chipps Island would not bias our estimation of fish origin because most juvenile 

Chinook Salmon were likely actively migrating downstream and observations of CWT 

individuals released at these locations are minimal.

To minimize the impact of unmarked hatchery releases at other locations, we estimated periods 

of time when individuals from these unmarked hatchery release groups likely occurred within the 

Delta. We considered all unmarked individuals observed while monitoring during these periods 

of time to have unknown origin. We estimated periods of occupancy within the Delta using the 

observed travel times of individual CWT fish released from each of the locations where groups 

containing only unmarked hatchery fish have been released (i.e., Battle Creek, Feather River, 

Sacramento River at Verona, and Sacramento River at Red Bluff Diversion Dam) to the entry 

(Sacramento Trawl Site) and exit (Chipps Island Trawl Site) locations of the Delta (Table 1). To 

incorporate uncertainty, we defined the periods of occupancy using the time (i.e., days) between 

when the first and last 2.5% of marked fish were detected at either Sacramento or Chipps Island 

relative to the release date of unmarked hatchery groups (Table 1). CWT fish released in the 

Sacramento River at Verona and the Red Bluff Diversion Dam took longer to reach the Chipps 

Island and Sacramento trawl sites than CWT fish released at Battle Creek or Feather River. The 

longer travel times may have been the result of fewer observations of CWT fish originating from 
21

the Sacramento River at Verona and the Red Bluff Diversion Dam release sites, resulting in 

higher uncertainty in the estimated days of occupancy within the Delta. Alternatively, the 

releases at Verona and the Red Bluff Diversion Dam may have contained higher proportions of 

fry (Pat Brandes, USFWS, personal communication), which move less quickly through the Delta 

than smolts (Kjelson et al. 1982) and may have caused the longer travel times. 

Table 1. The estimated period (days) of occupancy of CWT fish between when CWT fish were

released at locations where unmarked releases occurred and captured at the Chipps Island and 

Sacramento trawl sites during the 2000–2013 field seasons. 

Release 

location

Capture 

location 

(trawl site)

N (# of 

CWT fish

observed)

Days between 

capture of first 

2.5% of fish 

and release date

Days between 

capture of last 

2.5% of fish 

and release date

Estimated 

days of 

occupancy 

within Delta

Battle 

Creek

Chipps 

Island 3613 7 30

25

Sacramento 2223 5 21

Feather 

River

Chipps 

Island 1292 4 33

33

Sacramento 190 2 35

Sacramento 

River at 

Verona

Chipps 

Island 67 24 76

74

Sacramento 107 2 28

Sacramento 

River at 

Red Bluff 

Diversion 

Dam

Chipps 

Island 121 28 75

71

Sacramento 30 4 66

Relative Abundance Calculations

We standardized the samples collected within a day for each assemblage and for the origin 

groups of winter-run and the fall-, late fall-, and spring-run group of juvenile Chinook Salmon to 

catch-per-unit effort (CPUE) as fish per unit volume sampled (fish/10,000 m3) using the 

following equations:

Seine CPUEd =

∑(Catchs)

∑(0.5 · Depths

· Widths· Lengths)

· 10,000 ( 3 )
22

Trawl CPUEd =

∑(Catchs)

∑(Distance traveleds

· Net mouth area)

· 10,000 ( 4 )

where s indexes individual samples (i.e., a beach seine haul or trawl tow), and d indexes sample 

days. 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 0.5 multiplied by the depth. 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). 

We examined the spatial and temporal trends of the relative abundance by averaging and 

comparing CPUE estimates at monthly and yearly scales. The primary assumption associated 

with these CPUE comparisons is that gear efficiency (i.e., detection probabilities) is constant 

over time at each trawl or seine site, and comparable among trawl sites and seine regions. We 

treated Chinook Salmon races and origin groups or assemblage groups, seine regions, trawl sites, 

and gear types separately for 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 weekly, monthly, and yearly CPUE averages to minimize the overweighting 

of sample days and/or locations. To limit the bias of diel effects or variable gear efficiency on 

CPUE value comparisons, we only averaged samples collected between 07:00 am and 04:00 pm, 

and excluded those of poor condition (i.e., compromised gear deployment) within our

calculations. 

The mean weekly CPUE was calculated for each trawl site and seine region as the sum of the 

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. However, sample 

weeks including the first or last day of the field season only included days falling within the field 

season. 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 last sample week of September and March of the 2013 field season included September 1 or 

March 1, respectively, which is when we switched between gear types (MWTR and KDTR) at 

the Sacramento Trawl Site. Therefore, we presented the monthly CPUE averages for both KDTR 

and MWTR samples during September and March of the 2013 field season. This also resulted in 

the KDTR CPUE for September and the MWTR CPUE for March of the 2013 field season at the 

Sacramento Trawl Site being each generated from only 3 sample days, occurring in 1 week. The 

mean yearly CPUE was calculated as the sum of the mean monthly CPUE for a trawl site or 
23

seine region during each field season divided by the number of months sampled each field 

season.

We calculated and graphed the mean monthly CPUE of Chinook Salmon and assemblage groups 

to make intra-annual comparisons during the 2012 and 2013 field seasons. For inter-annual

comparisons of CPUE for juvenile Chinook Salmon and assemblage groups, we calculated and 

graphed mean yearly CPUE values starting in the 2000 field season for most trawl sites and seine 

regions. Confidence limits were omitted from the CPUE figures since uncertainty could not be 

accurately quantified after the computational series of averages. Thus, values presented are 

estimates and may incorporate a high degree of uncertainty.

In general, sampling methods have remained consistent from the 2000 field season to the present, 

including year-round sampling and standardized methods and gears. However, we calculated

mean yearly CPUE values for the Mossdale Trawl Site only during the 2004 through 2013 field 

seasons for juvenile Chinook Salmon and assemblage groups because the start of year-round

collaborative sampling with the CDFW 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. We did not report April through June data prior to 2004 because the DJFMP was not 

involved in the sampling, and these data have been already reported annually by the CDFW. We 

also calculated mean yearly CPUE values during the 1995 through 2013 field seasons year-round 

for both race groups of juvenile Chinook Salmon at the Chipps Island Trawl Site, based on 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. We calculated mean yearly CPUE values using April 

through June at the Chipps Island Trawl Site during the 1978 through 2013 field seasons for 

juvenile fall-, late fall-, and spring-run Chinook Salmon to extend our historical coverage. 

Though the relative abundances for the fall-, late fall-, and spring-run race groups are not 

presented individually, the total catch of each race of juvenile Chinook Salmon caught in the 

2012 and 2013 field seasons can be found in Tables A.3 and A.4.

Absolute Abundance Calculation

The absolute abundances of juvenile Chinook Salmon of each origin group of winter-run and the 

combined fall-, late fall-, and spring-run group immigrating into and emigrating out of the Delta

were estimated on a monthly scale from the 1978 to 2013 field seasons using the data collected 

at the Sacramento, Mossdale, and Chipps Island trawl sites. Annual comparisons of the absolute 

abundance of juvenile Chinook Salmon were limited to years and months when sampling was 

relatively consistent. The monthly absolute abundance (N) of (1) marked, (2) natural origin, (3) 

hatchery origin, and (4) unknown origin juvenile Chinook Salmon for both the juvenile winterrun, and fall-, late fall-, and spring-run groups were estimated using the methods modified from 

USFWS (1987) as:

Ni =

ni

ti· TRR ̅̅̅̅̅̅

( 5 )
24

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

during a month, ti represents the fraction of time the trawl site was sampled during a month, and 

TRR ̅̅̅̅̅̅ represents the mean trawl recovery rate at the trawl site. The assumption of this approach is 

that juvenile salmon are equally distributed in time as they migrate past the trawl sites and are 

never recaptured. It also assumes that the efficiency of the trawls is constant in space (i.e., 

throughout all sampling conditions) and time (i.e., within and among months).

The trawl recovery rate (TRR) for the Chipps Island trawl was estimated using the capture of 

CWT juvenile Chinook Salmon released approximately 10 and 12 km upstream of the Chipps 

Island Trawl Site at Sherman Island or Jersey Point. We estimated the TRR for the Sacramento 

trawl using the capture of CWT juvenile Chinook Salmon released approximately 4 and 8 km 

upstream of the Sacramento Trawl Site at Miller Park and the Broderick Boat Ramp, 

respectively. The TRR was calculated separately for the MWTR and KDTR nets used at the 

Sacramento Trawl Site to reflect possible differences in net efficiency. Lastly, we estimated the 

TRR for the Mossdale trawl using the capture of CWT and dye marked juvenile Chinook Salmon

released approximately 3 km upstream of the Mossdale Trawl Site at Mossdale Crossing. The 

TRR for each trawl site was calculated as:

TRRk =

nrecovered

navailable

( 6 )

where k indexes release groups at a release site, nrecovered represents the total number of CWT

juvenile Chinook Salmon within a release group collected at the trawl site, and navailable

represents the number of CWT juvenile Chinook Salmon within a release group available for 

collection at the 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:

navailable = nreleased · t ( 7 )

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

group and t represents the fraction of time the 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 similarly tagged or marked (CWT or spray dyed)

juvenile Chinook Salmon that had the same hatchery origin and were released at the same 

location and time. A total of 102 CWT releases have occurred at Sherman Island or Jersey Point 

between the 1989 to 2013 field seasons. Forty-seven CWT releases have occurred at Miller Park 

and Broderick Boat Ramp between the 1988 and 2009 field seasons. We calculated the TRR ̅̅̅̅̅̅ for 

the Chipps Island Trawl Site and the Sacramento Trawl Site using the recoveries from all the 

groups released at Sherman Island and Jersey Point, and at Miller Park and Broderick Boat 

Ramp, respectively, to maximize sample size and obtain a more robust estimate. The average 

fork lengths for the release groups near Chipps Island and Sacramento trawl sites ranged from 

70–179 mm and 56–138 mm, respectively, which corresponds to the majority of unmarked 
25

juvenile Chinook Salmon historically collected at these locations. All CWT release group data 

were obtained through the Regional Mark Information System (PSMFC 2014).

A total of five CWT releases have occurred at Mossdale Crossing since the 2003 field season.

There were two releases that were listed as Jersey Point, however RMIS notes that a proportion 

of the fish were released at Mossdale due to truck malfunction (PSMFC 2014). These fish were 

not included in the efficiency estimate because of the uncertainty associated with their release 

information. In addition, the CDFW has released 48 stain dye marked groups of hatchery reared

juvenile Chinook Salmon at Mossdale Crossing to estimate trawl efficiency at the Mossdale 

Trawl Site since the 1997 field season (SJRGA 2009; Steve Tsao, CDFW, personal 

communication). To maximize sample size, we estimated the TRR ̅̅̅̅̅̅ for the Mossdale Trawl Site 

using the recoveries of all CWT and spray dye release groups. Although the stain dye releases

often reused marks (i.e., dye colors) within seasons, these releases were spaced at least 7 days 

apart and we determined that approximately 98% of CWT individuals released at Mossdale 

Crossing were detected at the Mossdale Trawl Site within 7 days from being released. 

The TRR ̅̅̅̅̅̅ was calculated for each trawl site 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 TR̅̅̅̅̅R̅ and its 95% confidence 

interval (CI). The intervals should be considered minimum confidence limits because they only 

incorporate the uncertainty associated with the TRR ̅̅̅̅̅̅ estimates. We calculated absolute 

abundance estimates at the Chipps Island Trawl Site from April through June during the 1978 

through 2013 field seasons for fall-, late fall-, and spring-run juvenile Chinook Salmon. We also 

calculated annual absolute abundance estimates during the 1995–2013, 2000–2013, and 2004–

2013 field seasons at the Chipps Island, Sacramento, and Mossdale trawl sites, respectively, for 

both winter-run and the fall-, late fall-, and spring-run group of Chinook Salmon.

Length Frequency

We plotted length frequency distributions for all unmarked juvenile Chinook Salmon during the 

2012 and 2013 field seasons for each seine region and trawl site. In cases where Chinook Salmon

were “plus counted” (i.e., only counted and 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 categorized the race of unmarked 

juvenile Chinook Salmon using the river LDC, 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. 

 

River Flow Conditions

River flow data were obtained from the USGS and CDWR (USGS 2014; CDWR 2014a). 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, 
26

estimates of the daily Delta outflow past Chipps Island towards the San Francisco Bay, which 

takes into account water exports, were obtained from Dayflow (CDWR 2014a). We also 

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

the California Data Exchange Center (CDWR 2014b). 

We presented the mean monthly CPUE of Chinook Salmon races and fish assemblage groups

along with mean monthly discharge during the 2012 and 2013 field seasons. Similarly, we 

compared the yearly CPUE of Chinook Salmon races and fish assemblage groups along with 

mean yearly discharge at each trawl site and seine region. The CPUE of fishes within the Lower 

Sacramento River Seine Region, 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. These comparisons were selected to broadly represent what 

fish experience, in terms of average daily flow, at the sampling locations.

Results and Discussion

During the 2012 and 2013 field seasons, 8,659 trawl samples were collected without any severe 

gear malfunctions. We completed 2,306 trawls at the Chipps Island Trawl Site, 3,496 trawls at 

the Mossdale Trawl Site, and 2,857 trawls at the Sacramento Trawl Site. The trawl tows were 

evenly distributed throughout the 2012 and 2013 field seasons (Tables A.5 and A.6). As a result, 

we considered the inter- and intra-annual trawl catch comparisons robust due to minimal spatial 

and temporal bias. 

During the 2012 and 2013 field seasons, 4,005 seine samples were collected without any severe 

gear malfunctions. There was considerable spatial and temporal variability in the number of 

samples collected at sites within nearly all seine regions during the 2012 and 2013 field seasons

(Tables A.7–A.18), similar to the 2010 and 2011 field seasons (Speegle et al. 2013). For 

example, on average approximately 46% and 49% of the historically sampled sites within the 

South Delta Seine Region were effectively sampled during sample weeks within the 2012 and 

2013 field seasons, respectively (Tables A.13 and A.14). The number of samples collected 

within the South Delta Seine Region during the 2012 (n=246) and 2013 (n=261) field seasons

were considerably lower than the previous decade's annual average (x=329, SE=15.7). In 

addition, on average approximately 44% and 62% of the historically sampled sites within the 

Lower San Joaquin Seine Region were effectively sampled during sample weeks within the 2012 

and 2013 field seasons, respectively (Tables A.15 and A.16). As a result, catch data associated 

with these seine regions may contain both inter- and intra-annual bias. 

Throughout the 2012 and 2013 field seasons, the inability to effectively sample seine sites 

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

and low river discharge (Table A.19). The DJFMP is currently investigating the feasibility of 

implementing a stratified random sampling design for boat electrofishing to supplement beach 

seining within the San Francisco Estuary. New sampling methods are needed to re-establish and 
27

ensure future continuity of non-biased representative catch data within near-shore littoral habitats 

within the lower rivers and Delta.

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 documents the presence of fishes at 

a given time and location (Tables A.5–A.18). However, detection probability and the probability 

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

Water Quality

We collected 43,052 water quality samples during the 2012 and 2013 field seasons: 12,619 water 

temperature, 10,393 conductivity, 10,313 dissolved oxygen, and 9,727 turbidity samples. The 

intra-annual variability in water temperature was consistent among the beach seine regions and 

trawl sites during the 2012 and 2013 field seasons (Figures 8 and 9). Temperature ranged from 

4.4 to 27.4°C among our seine regions and trawl sites during the 2012 field season and 4.7 to 

30.2°C during the 2013 field season. Water temperatures, on average, were highest within the 

lower San Joaquin River and South Delta regions relative to other regions during the summer of 

both field seasons. Further, the summer temperatures were, on average, higher during the 2013 

field season relative to the 2012 field season within the lower San Joaquin River and South 

Delta. Temperatures often exceeded 25°C during the summer (June through August) of the 2013

field season, a critically dry year within the San Joaquin River Basin (Table A.19).

We observed dissolved oxygen values ranging from 2.3 to 17.3 mg/L among our seine regions 

and trawl sites during the 2012 field season and 1.4 to 19.5 mg/L among our seine regions and 

trawl sites during the 2013 field season (Figures 10 and 11). In general, dissolved oxygen was 

highest during the winter season and lowest during the summer season for all seine regions and 

trawl sites during both field seasons. On average, dissolved oxygen varied more within the 

Lower San Joaquin River and South Delta seine regions, and at the Mossdale Trawl Site from 

May to August during both field seasons. During the 2013 field season, we observed the 

dissolved oxygen increase to above 12 mg/L at the Mossdale Trawl Site starting in May and 

decrease to less than 3 mg/L during June and July. This is likely due to agricultural nutrient 

inputs supporting increased primary production followed by increased bacterial respiration 

supported by excess nutrients or increased detritus from aquatic plants and algae (Dunne and 

Leopold 1978).

Turbidity samples ranged from 2 to 638 NTU and 1 to 384 NTU during the 2012 and 2013 field 

seasons, respectively (Figures 12 and 13). In general, the turbidity was lower within the Central 

Delta and South Delta seine regions relative to other regions throughout most of the year. In 

addition, the turbidity varied considerably within the San Pablo Bay Seine Region possibly due 

to wind and wave erosion during the spring and summer seasons. We also observed increased

turbidity in December during the 2013 field season in all seine regions and trawl sites, possibly

resulting from increased precipitation and discharge. 
28

Conductivity varied considerably among trawls sites and seine regions during the 2012 and 2013 

field seasons (Figures 14 and 15). We observed that conductivity was highest across all months

within the San Francisco and San Pablo Bay Seine Region. This was expected because the San 

Francisco and San Pablo Bay Seine Region is the closest in proximity to the Pacific Ocean and is

the seine region most similar to a marine environment. Conversely, the conductivity within the 

Lower Sacramento River and North Delta seine regions, and at the Sacramento and Mossdale 

trawl sites, were lower and more consistent relative to other monitoring locations, which may be 

due to these sites being less exposed to tidal exchange. The conductance within the South Delta 

and lower San Joaquin River seine regions, and at the Chipps Island Trawl Site, were the most 

variable within and among months, possibly due to agricultural inputs, water operations, and 

tidal exchange. Little distinct inter-annual patterns were observed. 
29

Figure 8. Water temperature data collected by month during sampling at the (A) Chipps Island (C), Sacramento (S), and Mossdale (M)

trawl sites and within the (B) Lower Sacramento River (Region 1), North Delta (Region 2), Central Delta (Region 3), South Delta 

(Region 4), Lower San Joaquin River (Region 5), and San Francisco and San Pablo Bay (Region 6) seine regions during the 2012 field 

season. The boxes represent the 25th and 75th percentiles, the line within the box represents the median, the whiskers represent the 10th

and 90th percentiles, and points represent outliers.

(B) 2012 field season

Beach seine regions

0

5

10

15

20

25

30

35

Region 2

(A) 2012 field season

Trawl sites

Water temperature (°C)

0

5

10

15

20

25

30

35 Chipps Island Trawl Site

Sacramento Trawl Site

Mossdale Trawl Site

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

C S M

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

1 2 3 4 5 6 

C S M C S M C S M C S M C S M C S M C S M C S M C S M C S M C S M

1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 

Region 1

Region 2

Region 3

Region 4

Region 5

Region 6
30

Figure 9. Water temperature data collected by month during sampling at the (A) Chipps Island (C), Sacramento (S), and Mossdale (M)

trawl sites and within the (B) Lower Sacramento River (Region 1), North Delta (Region 2), Central Delta (Region 3), South Delta 

(Region 4), Lower San Joaquin River (Region 5), and San Francisco and San Pablo Bay (Region 6) seine regions during the 2013 field 

season. The boxes represent the 25th and 75th percentiles, the line within the box represents the median, the whiskers represent the 10th

and 90th percentiles, and points represent outliers.

d

d

d

(B) 2013 field season

Beach seine regions

0

5

10

15

20

25

30

35

Region 2

(A) 2013 field season

Trawl sites

Water temperature (°C)

0

5

10

15

20

25

30

35

Chipps Island Trawl Site

Sacramento Trawl Site

Mossdale Trawl Site

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

C S M

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

1 2 3 4 5 6 

C S M C S M C S M C S M C S M C S M C S M C S M C S M C S M C S M

1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 

Region 1

Region 2

Region 3

Region 4

Region 5

Region 6
31

Figure 10. Dissolved oxygen data collected by month during sampling at the (A) Chipps Island (C), Sacramento (S), and Mossdale 

(M) trawl sites and within the (B) Lower Sacramento River (Region 1), North Delta (Region 2), Central Delta (Region 3), South Delta 

(Region 4), Lower San Joaquin River (Region 5), and San Francisco and San Pablo Bay (Region 6) seine regions during the 2012 field 

season. The boxes represent the 25th and 75th percentiles, the line within the box represents the median, the whiskers represent the 10th

and 90th percentiles, and points represent outliers. *Dissolved oxygen not sampled.

(B) 2012 field season

Beach seine regions

0

5

10

15

20

Region 2

(A) 2012 field season

Trawl sites

Dissolved oxygen (mg/L)

0

5

10

15

20

Chipps Island Trawl Site

Sacramento Trawl Site

Mossdale Trawl Site

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

C *S*M*

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

1 2 3 4 5 6 

C *S*M* C*S*M* C*S*M* C S M C S M C S M C S M C S M* C S M* C S M* C S M

1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 

Region 1

Region 2

Region 3

Region 4

Region 5

Region 6
32

Figure 11. Dissolved oxygen data collected by month during sampling at the (A) Chipps Island (C), Sacramento (S), and Mossdale 

(M) trawl sites and within the (B) Lower Sacramento River (Region 1), North Delta (Region 2), Central Delta (Region 3), South Delta 

(Region 4), Lower San Joaquin River (Region 5), and San Francisco and San Pablo Bay (Region 6) seine regions during the 2013 field 

season. The boxes represent the 25th and 75th percentiles, the line within the box represents the median, the whiskers represent the 10th

and 90th percentiles, and points represent outliers.

(B) 2013 field season

Beach seine regions

0

5

10

15

20

Region 2

(A) 2013 field season

Trawl sites

Dissolved oxygen (mg/L)

0

5

10

15

20 Chipps Island Trawl Site

Sacramento Trawl Site

Mossdale Trawl Site

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

C S M

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

1 2 3 4 5 6 

C S M C S M C S M C S M C S M C S M C S M C S M C S M C S M C S M

1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 

Region 1

Region 2

Region 3

Region 4

Region 5

Region 6
33

Figure 12. Turbidity data collected by month during sampling at the (A) Chipps Island (C), Sacramento (S), and Mossdale (M) trawl 

sites and within the (B) Lower Sacramento River (Region 1), North Delta (Region 2), Central Delta (Region 3), South Delta (Region 

4), Lower San Joaquin River (Region 5), and San Francisco and San Pablo Bay (Region 6) seine regions during the 2012 field season. 

The boxes represent the 25th and 75th percentiles, the line within the box represents the median, the whiskers represent the 10th and 90th

percentiles, and points represent outliers. *Turbidity not sampled.

(B) 2012 field season

Beach seine regions

0

100

200

300

400

500

Region 1

Region 2

Region 3

Region 4

Region 5

Region 6

Region 2

(A) 2012 field season

Trawl sites

Turbidity (NTU)

0

100

200

300

400

500

Chipps Island Trawl Site

Sacramento Trawl Site

Mossdale Trawl Site

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

C S*M*

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

C S*M* C S*M* C S*M* C S M C S M C S M C S M C S M* C S M* C S M* C S M

(1 2 3 4 5 6)* (1 2 3 4 5 6)* (1 2 3 4 5 6)* (1 2 3 4 5 6)* (1 2 3 4 5 6)* 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 
34

Figure 13. Turbidity data collected by month during sampling at the (A) Chipps Island (C), Sacramento (S), and Mossdale (M) trawl 

sites and within the (B) Lower Sacramento River (Region 1), North Delta (Region 2), Central Delta (Region 3), South Delta (Region 

4), Lower San Joaquin River (Region 5), and San Francisco and San Pablo Bay (Region 6) seine regions during the 2013 field season. 

The boxes represent the 25th and 75th percentiles, the line within the box represents the median, the whiskers represent the 10th and 90th

percentiles, and points represent outliers.

(B) 2013 field season

Beach seine regions

0

100

200

300

400

500

Region 2

(A) 2013 field season

Trawl sites

Turbidity (NTU)

0

100

200

300

400

500

Chipps Island Trawl Site

Sacramento Trawl Site

Mossdale Trawl Site

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

C S M

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

1 2 3 4 5 6 

C S M C S M C S M C S M C S M C S M C S M C S M C S M C S M C S M

1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 

Region 1

Region 2

Region 3

Region 4

Region 5

Region 6
35

Figure 14. Conductivity data collected by month during sampling at the (A) Chipps Island (C), Sacramento (S), and Mossdale (M)

trawl sites and within the (B) Lower Sacramento River (Region 1), North Delta (Region 2), Central Delta (Region 3), South Delta 

(Region 4), Lower San Joaquin River (Region 5), and San Francisco and San Pablo Bay (Region 6) seine regions during the 2012 field 

season. The boxes represent the 25th and 75th percentiles, the line within the box represents the median, the whiskers represent the 10th

and 90th percentiles, and points represent outliers. The y-axis is presented on a common log scale. *Conductivity not sampled.

(B) 2012 field season; beach seine regions

10

100

1000

10000

100000

(A) 2012 field season

Trawl sites

Conductivity (μS/cm, log)

10

100

1000

10000

100000

Chipps Island Trawl Site

Sacramento Trawl Site

Mossdale Trawl Site

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

1 2 3 4 5 6 

C S M C S M C S M C S M C S M* C S M* C S M* C S M

1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 

Region 1

Region 2

Region 3

Region 4

Region 5

Region 6

C*S*M* C *S*M* C* S*M* C*S*M*

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

1,000

10,000

100,000

1,000

10,000

100,000
36

Figure 15. Conductivity data collected by month during sampling at the (A) Chipps Island (C), Sacramento (S), and Mossdale (M)

trawl sites and within the (B) Lower Sacramento River (Region 1), North Delta (Region 2), Central Delta (Region 3), South Delta 

(Region 4), Lower San Joaquin River (Region 5), and San Francisco and San Pablo Bay (Region 6) seine regions during the 2013 field 

season. The boxes represent the 25th and 75th percentiles, the line within the box represents the median, the whiskers represent the 10th

and 90th percentiles, and points represent outliers. The y-axis is presented on a common log scale. 

(B) 2013 field season; beach seine regions

10

100

1000

10000

100000

(A) 2013 field season

Trawl sites

Conductivity (μS/cm, log)

10

100

1000

10000

100000

Chipps Island Trawl Site

Sacramento Trawl Site

Mossdale Trawl Site

Region 1

Region 2

Region 3

Region 4

Region 5

Region 6

1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 

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

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

C S M C S M C S M C S M C S M C S M C S M C S M C S M C S M C S M C S M

1,000

10,000

100,000

1,000

10,000

100,000
37

Fish Assemblage

A total of 355,181 fishes, representing 83 species, was collected within samples (beach seines 

and trawls) used for assemblage analyses during the 2012 and 2013 field seasons (does not 

include marked or unidentified fish; Tables A.3 and A.4). Sixty-five percent (n=229,145) of the 

fishes were observed during the 2013 field season. Approximately 70% (n=88,373) and 81% 

(n=184,648) of the fishes captured during the 2012 and 2013 field seasons, respectively, were 

identified as species not native to the San Francisco Estuary. Of the 83 species observed, the

most abundant species were the Inland Silverside Menidia beryllina, juvenile Chinook Salmon, 

Red Shiner Cyprinella lutrensis, Sacramento Sucker, American Shad Alosa sapidissima, and 

Threadfin Shad Dorosoma petenense, which together comprised 74% and 87% of the total catch 

during the 2012 and 2013 field seasons, respectively. 

In general, anadromous-pelagic-nonnative fishes dominated the catch at the Chipps Island Trawl 

Site during the 2012 and 2013 field seasons (Figure 16). Within this group, the American Shad 

was the most common species observed at the Chipps Island Trawl Site, and comprised 79% 

(n=19,959) and 63% (n=9,866) of the fishes captured during the 2012 and 2013 field seasons, 

respectively (Tables A.3 and A.4). Anadromous-pelagic-nonnative fishes (e.g., American Shad) 

dominated the catch at the Chipps Island Trawl Site from July to December (Figure 16). 

However, we observed that anadromous-pelagic-native fishes (e.g., juvenile Chinook Salmon) 

dominated the catch during most of the months between December and May. The mean yearly 

CPUE estimates suggested that anadromous-pelagic-native fishes have declined steadily at the 

Chipps Island Trawl Site since the 1996 field season. Anadromous-pelagic-nonnative fishes have 

also declined during this period; however this group appears to respond positively to improved 

outflow conditions. 

During the 2012 and 2013 field seasons, the most common species captured at the Sacramento 

Trawl Site was juvenile Chinook Salmon (82%, n=4,788; Tables A.3 and A.4). We observed that 

these anadromous-pelagic-native fishes were generally captured between November and June, 

and their CPUE peaked in April during both field seasons (Figure 17). However, some nonnative 

anadromous and resident pelagic fishes were observed in relatively low densities from August to 

February. The mean yearly CPUE of anadromous-pelagic-native fishes has increased annually at 

the Sacramento Trawl Site since the 2010 field season. However, the mean yearly CPUE 

estimate remains below the 2000 to 2011 average (MWTR=7.38, KDTR=3.54). 

The Inland Silverside was overall the most common species observed and comprised 55% 

(n=162,542) of the fishes captured at the Mossdale Trawl Site and in the Lower Sacramento 

River, North Delta, Central Delta, South Delta, and Lower San Joaquin River seine regions 

during the 2012 and 2013 field seasons (Tables A.3 and A.4). As a result, the pelagic-nonnative 

fishes dominated the observed fish assemblage within the Mossdale Trawl Site and most seine 

regions throughout both field seasons (Figures 18–20). We observed the majority of fishes at the 

Mossdale Trawl Site in July during both field seasons (Figure 18). This may be due to increased 

primary productivity within the lower San Joaquin River as indicated by dissolved oxygen 

samples (Figures 12 and 13). In general, pelagic-nonnative fishes dominated the observed 

assemblage in nearly all months at the Mossdale Trawl Site except April and May when 

anadromous-pelagic-native fishes (e.g., juvenile Chinook Salmon) were present. In addition to 
38

pelagic-nonnative fishes, the mean monthly CPUE estimates suggest that the fish assemblage 

within the North Delta and Lower Sacramento River seine regions contained considerable 

densities of anadromous-pelagic-native fishes from January to March and benthic-native fishes

(e.g., lamprey and Sacramento Sucker; Tables A.3 and A.4) from April to July (Figure 19). The 

mean yearly CPUE estimates among beach seine regions and the Mossdale Trawl demonstrated

that fish densities for most assemblage groups were relatively low during the 2012 field season

and increased slightly in the 2013 field season, excluding the pelagic-nonnative fishes group 

which sharply increased in 2013 compared to past years (Figures 18 and 20).

Within the San Francisco and San Pablo Bay Seine Region, the Topsmelt Atherinops affinis was 

the most common fish species observed and comprised 68% (n=9,260) of all fishes captured

during both the 2012 and 2013 field seasons (Tables A.3 and A.4). The mean monthly CPUE 

estimates suggested that pelagic-nonnative fishes were observed in higher proportions within and 

among all field seasons relative to other assemblages groups (Figures 19 and 20). Nearly all 

fishes observed within this seine region, including Topsmelt, are considered marine fish 

presumably due to the higher conductivity within the region (Figures 14 and 15). In general, we 

cannot discern any temporal patterns from monthly or yearly CPUE estimates in this region for 

any fish assemblage group due to relatively low catch numbers. 

There was an overall increase of nonnative fishes captured during the 2013 field season from the 

2012 field season (n=184,648 and n=88,373, respectively; Tables A.3 and A.4). Many of the 

nonnative resident fishes that dominated our assemblage groups (e.g., Inland Silverside and Red 

Shiner) originate from unstable, stagnant, warm water environments (Moyle 2002). The 2013 

field season was the second year of drought (Table A.19), which may have produced water 

quality conditions more favorable to these species. Likely for this reason, we observed that water 

temperatures generally increased in the 2013 field season relative to the 2012 field season, 

particularly within the South Delta and San Joaquin River seine regions (Figures 8 and 9). 

Further, we determined that the 2013 field season had the highest proportion of nonnative 

resident fishes, especially within the South Delta and Lower San Joaquin River seine regions

(Figure 20).

The overall higher densities of fishes in the 2013 field season correspond to a higher peak flow 

occurring earlier in the year than in 2012 (around 1400 m3/sec in December of the 2013 field 

season for Delta Outflow and the discharge at the Sacramento River at Freeport versus 800 

m

3

/sec in April of 2012; Figures 16–20). The increased discharge observed at the Sacramento 

Trawl Site in 2013 may also explain the earlier occurrence of anadromous-pelagic-native fishes. 

In contrast, the increased outflow in March through April may explain the overall increased fish 

densities captured at Chipps Island in 2012. The later flows in the 2012 field season may have 

also extended the occurrence of the anadromous-pelagic-native fishes in the beach seines (Figure 

20).
39

Figure 16. The mean monthly and yearly CPUE (bars) of juvenile fish assemblages captured in 

MWTRs at the Chipps Island Trawl Site, and the estimated mean monthly and yearly Delta 

outflow (solid line) during the (A) 2012, (B) 2013, and (C) 1995 through 2013 field seasons. 

(C) 1995–2013 field seasons 

Mean discharge (m

3/sec)

1,000

1,200

1,400

1,600

1,800

1,000

1,200

1,400

1,600

1,800

1,000

1,200

1,400

1,600

1,800
40

Figure 17. The mean monthly and yearly CPUE of juvenile fish assemblages captured in 

MWTRs (solid bars) and KDTRs (striped bars) at the Sacramento Trawl Site, and the mean 

monthly and yearly Sacramento River discharge at Freeport (solid line) during the (A) 2012, (B)

2013, and (C) 2000 through 2013 field seasons. 

(C) 2000–2013 field seasons 

1,000

1,200

1,400

1,000

1,200

1,400

1,000

1,200

1,400

Mean discharge (m

3/sec)
41

Figure 18. The mean monthly and yearly CPUE (bars) of juvenile fish assemblages captured in 

KDTRs at the Mossdale Trawl Site, and the mean monthly and yearly San Joaquin River 

discharge at Vernalis (solid line) during the (A) 2012, (B) 2013, and (C) 2004 through 2013 field 

seasons.

(C) 2004–2013 field seasons 

Mean discharge (m

3/sec)
42

Figure 19. The mean monthly CPUE (bars) of juvenile fish assemblages captured within the Lower Sacramento River (1), North Delta 

(2), Central Delta (3), South Delta (4), Lower San Joaquin River (5), and San Francisco and San Pablo Bay (6) beach seine regions, 

and the estimated mean monthly and yearly Delta outflow (dashed line), Sacramento River discharge at Freeport (solid line), and San 

Joaquin River discharge at Vernalis (dotted line) during the (A) 2012 and (B) 2013 field seasons.

1,000

1,200

1,400

1,000

1,200

1,400

20,000

30,000

40,000

50,000

60,000

10,000

60,000

80,000

100,000

120,000

140,000

40,000

20,000

1 2345 6 1 2345 6 1 2345 6 1 2345 6 1 2345 6 1 2345 6 1 2345 6 1 2345 6 1 2345 6 1 2345 6 1 2345 6 1 2345 6

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

1 2345 6 1 2345 6 1 2345 6 1 2345 6 1 2345 6 1 2345 6 1 2345 6 1 2345 6 1 2345 6 1 2345 6 1 2345 6 1 2345 6

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

Mean discharge (m

3/sec)
43

Figure 20. The mean yearly CPUE (bars) of juvenile fish assemblages captured within the Lower Sacramento River (1), North Delta 

(2), Central Delta (3), South Delta (4), Lower San Joaquin River (5), and San Francisco and San Pablo Bay (6) beach seine regions, 

and the estimated mean monthly and yearly Delta outflow (dashed line), Sacramento River discharge at Freeport (solid line), and San 

Joaquin River discharge at Vernalis (dotted line) during the 2000 through 2013 field seasons.

1,800

40,000

60,000

80,000

100,000

120,000

20,000

1 234 56

 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 

1 234 56 1 234 56 1 234 56 1 234 56 1 234 56 1 234 56 1 234 56 1 234 56 1 234 56 1 234 56 1 234 56 1 234 56 1 234 56

Mean discharge (m

3/sec)

1,000

1,400

1,600

1,200
44

Juvenile Chinook Salmon

We captured 15,750 and 18,341 juvenile Chinook Salmon during the 2012 and 2013 field 

seasons, respectively (Tables A.3 and A.4). During the 2012 field season, 13,561 individuals 

were unmarked, of which 1% (n=167) were categorized as winter-run, 69% (n=10,944) as fallrun, 15% (n=2,407) as spring-run, and less than 1% (n=24) as late fall-run using the river LDC

or were not raced (n=19, Tables A.3 and A.4). Of the 2,189 marked (i.e., clipped adipose fin)

juvenile Chinook Salmon recovered during 2012, 97% (n=2,114) contained a readable CWT 

(Table A.20). During the 2013 field season, 16,968 individuals were unmarked, of which 2% 

(n=432) were categorized as winter-run, 78% (n=14,367) as fall-run, 12% (n=2,134) as springrun, and less than 1% (n=35) as late fall-run Chinook Salmon (Tables A.3 and A.4). Of the 1,373

marked juvenile Chinook Salmon recovered during 2013, 97% (n=1,339) contained a readable 

CWT (Table A.21). 

We recovered a total of 21 and 9 marked juvenile winter-run Chinook Salmon containing a CWT 

during the 2012 and 2013 field seasons, respectively, within the Lower Sacramento River Seine 

Region (2013 only), the Sacramento Trawl Site, and the Chipps Island Trawl Site (Tables A.20

and A.21). All recovered CWT winter-run Chinook Salmon were released by the Livingston 

Stone National Fish Hatchery, which released 194,264 (185,313 marked and with a CWT) and 

181,857 (169,967 marked and with a CWT) juvenile winter-run Chinook Salmon in the Central 

Valley during the 2012 and 2013 field seasons (PSMFC 2014). 

We recovered a total of 225 and 18 marked juvenile spring-run Chinook Salmon containing a 

CWT during the 2012 and 2013 field seasons, respectively, within the Lower Sacramento River, 

North Delta, and Central Delta seine regions, the Sacramento Trawl Site, and the Chipps Island 

Trawl Site (Tables A.20 and A.21). All recovered CWT spring-run Chinook Salmon were 

released by the Feather River Fish Hatchery, which released 2,244,989 (2,213,475 marked and 

with a CWT) and 2,159,071 (2,121,964 marked and with a CWT) juvenile spring-run Chinook 

Salmon in the Central Valley (49.5% and 52.1%) and the San Francisco area bays (50.5% and 

47.9%) during the 2012 and 2013 field seasons (PSMFC 2014). 

We recovered a total of 1,816 and 1,263 marked juvenile fall-run Chinook Salmon containing a 

CWT during the 2012 and 2013 field seasons, respectively, within the Lower Sacramento River, 

North Delta, Central Delta, South Delta, Lower San Joaquin River, and San Pablo Bay Area 

seine regions, the Sacramento Trawl Site, and the Chipps Island Trawl Site (Tables A.20 and 

A.21). In the 2012 field season, 33,877,856 (9,289,470 marked and with a CWT) hatchery reared 

juvenile fall-run Chinook Salmon were released into the Central Valley (67.6%) and the San 

Francisco area bays (32.4%) in the combined release efforts of the Coleman National Fish 

Hatchery (36.9%), Feather River Fish Hatchery (28.9%), Mokelumne River Fish Hatchery 

(19.3%), Nimbus Fish Hatchery (14.2%), and Merced River Fish Facility (0.8%; PSMFC 2014). 

In the 2013 field season, 28,057,046 (7,706,497 marked and with a CWT) hatchery reared 

juvenile fall-run Chinook Salmon were released into the Central Valley (75.8%) or the San 

Francisco area bays (24.2%) in the combined release efforts of the Coleman National Fish 

Hatchery (42.3%), Feather River Fish Hatchery (22.3%), Mokelumne River Fish Hatchery 

(18.7%), Nimbus Fish Hatchery (14.3%), and Merced River Fish Facility (2.4%; PSMFC 2014). 
45

We recovered a total of 52 and 140 marked juvenile late fall-run Chinook Salmon containing a 

CWT during the 2012 and 2013 field seasons, respectively, within the Lower Sacramento River

and North Delta seine regions, the Sacramento Trawl Site, and the Chipps Island Trawl Site 

(Tables A.20 and A.21). All recovered CWT late fall-run Chinook Salmon were released by the 

Coleman National Fish Hatchery, which released 1,053,282 (1,037,859 marked) and 1,094,288

(1,031,419 marked) juvenile late fall-run Chinook Salmon in the Central Valley during the 2012 

and 2013 field seasons (PSMFC 2014). 

Based on CWT recoveries during the 2012 and 2013 field seasons, there is evidence that races 

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

the Central and South Delta likely based on water diversions, exports, and tidal exchange (Tables 

A.20 and A.21). As a result, CWT recovery data further justifies our application of the river LDC

to identify the race of unmarked juvenile Chinook Salmon captured in all seine regions except 

the Lower San Joaquin River Seine Region.

Nearly all of the juvenile Chinook Salmon captured using beach seines since the 2000 field 

season were estimated to have natural origin (93.5% natural origin, 0.2% hatchery origin, 1.2% 

marked, 5.0% unknown origin). While hatcheries typically release smolt-sized fish and few fry 

(PSMFC 2014), both fry- and smolt-sized Chinook Salmon were observed in the beach seines 

(see “Fork Length Distributions” section). This suggested that hatchery juvenile Chinook Salmon 

may be less likely to occur in unobstructed near shore habitats within the San Francisco Estuary

than natural origin juvenile Chinook Salmon.

Winter-Run Distribution and Relative Abundance

In general, nearly 100% of all juvenile winter-run Chinook Salmon produced by the Livingston 

Stone National Fish Hatchery have been released marked and containing a CWT since 

production began in 1995 (PSMFC 2014). We estimated that natural juvenile winter-run sized 

Chinook Salmon were captured in relatively low numbers at the Chipps Island Trawl Site, the 

Sacramento Trawl Site, and in the Lower Sacramento River, North Delta, Central Delta, and 

South Delta seine regions during the 2012 and 2013 field seasons (Figures 21–24). Although

genetic analyses have determined that the river LDC is fairly accurate for winter-run Chinook 

Salmon designation, it should be noted that significant numbers of individuals from other races 

are included within the winter-run criteria (Pyper et al. 2013), thus the abundance is significantly 

over-estimated using the river LDC. 

Consistent with the 2010 and 2011 field seasons (Speegle et al. 2013), winter-run sized juvenile 

Chinook Salmon were generally captured from December through April at the Chipps Island 

Trawl Site and November through April at the Sacramento Trawl Site (Figures 21 and 22). The 

CPUE at the Sacramento Trawl Site peaked in March and November during the 2012 and 2013

field seasons, respectively. Conversely, the CPUE at the Chipps Island Trawl Site peaked in 

April and March during the 2012 and 2013 field seasons. There was generally only a one month 

time lag between the peak CPUE at the Sacramento Trawl Site (March) and the Chipps Island 

Trawl Site (April) during the 2012 field season, which occurred during the time of peak 

Sacramento River discharge into the Delta. However, there was a four month time lag between 
46

the peak CPUE at the Sacramento Trawl Site (November) and the Chipps Island Trawl Site 

(March) during the 2013 field season. The Sacramento River discharge, on average, peaked in 

November during the 2013 field season. This may indicate that residency time within the Delta is 

likely influenced by the interaction between the size of fish entering the Delta and the timing of 

peak Sacramento River discharge into the Delta within the year. The mean yearly CPUE at the 

Sacramento Trawl Site has increased considerably since the record low observed during the 2011 

field season (Figure 22), whereas the mean yearly CPUE at the Chipps Island Trawl Site was

near the record low during both the 2012 and 2013 field seasons (Figure 21). The data in 2012 

and 2013 suggested that increased residency time in the Delta may not correspond to higher 

numbers of Chinook Salmon emigrating out of the Delta. However, the relative abundance 

between years is likely masked by the variation in the large numbers of false positives contained 

within the winter-run LDC. 

Estimated natural winter-run sized Chinook Salmon were captured using beach seines in most 

months from October through March during the 2012 and 2013 field seasons (Figure 23). We did 

not observe any marked fish in beach seines during the 2012 field season. We observed marked

fish only during the month of February within the North Delta Seine Region during the 2013 

field season, which corresponds with hatchery releases within the watershed. In 2013, the mean 

monthly CPUE of natural winter-run juveniles peaked in the Lower Sacramento River and North 

Delta seine regions in January compared to December during the 2012 field season (Figure 23). 

Conversely, the monthly CPUE in the Central Delta and South Delta seine regions peaked either 

in February (2013) or March (2012). The mean yearly CPUE estimates suggested that natural 

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 24). 
47

Figure 21. The mean monthly and yearly CPUE (bars) of juvenile winter-run Chinook Salmon 

captured in MWTRs at the Chipps Island Trawl Site, and the estimated mean monthly and yearly 

Delta outflow (solid line) during the (A) 2012, (B) 2013, and (C) 1995 through 2013 field 

seasons.

(C) 1995–2013 field seasons 

1,000

1,200

1,400

1,600

1,800

1,000

1,200

1,400

1,600

1,800

1,000

1,200

1,400

1,600

1,800

Mean discharge (m

3/sec)
48

Figure 22. The mean monthly and yearly CPUE of juvenile winter-run Chinook Salmon captured 

in MWTRs (solid bars) and KDTRs (striped bars) at the Sacramento Trawl Site, and the mean 

monthly and yearly Sacramento River discharge at Freeport (solid line) during the (A) 2012, (B)

2013, and (C) 2000 through 2013 field seasons. 

(C) 2000–2013 field seasons 

1,000

1,200

1,400

1,000

1,200

1,400

Mean discharge (m

3/sec)

1,000

1,200

1,400
49

Figure 23. The mean monthly CPUE (bars) of juvenile winter-run Chinook Salmon captured within the Lower Sacramento River (1), 

North Delta (2), Central Delta (3), South Delta (4), Lower San Joaquin River (5), and San Francisco and San Pablo Bay (6) beach

seine regions, and the estimated mean monthly and yearly Delta outflow (dashed line), Sacramento River discharge at Freeport (solid 

line), and San Joaquin River discharge at Vernalis (dotted line) during the (A) 2012 and (B) 2013 field seasons.

Mean discharge (m

3

1,000

/sec)

1,000

1,200

1,400

1,000

1,200

1,400

1 234 56

1 234 56 1 234 56 1234 56

1234 56

1234 56 1 234 56

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

1 234 56 1 234 56 1 234 56 1 234 56 1234 56 123456 1 234 56 1 234 56 1 234 56 1 234 56

1 234 56 1 23456 1 234 56 1 234 56 1 234 56 1 234 56 1 234 56

Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul 
50

Figure 24. The mean yearly CPUE (bars) of juvenile winter-run Chinook Salmon captured within the Lower Sacramento River (1), 

North Delta (2), Central Delta (3), South Delta (4), Lower San Joaquin River (5), and San Francisco and San Pablo Bay (6) beach 

seine regions, and the estimated mean monthly and yearly Delta outflow (dashed line), Sacramento River discharge at Freeport (solid 

line), and San Joaquin River discharge at Vernalis (dotted line) during the 2000 through 2013 field seasons.

Mean discharge (m

3/sec)

1,000

1,200

1,400

1,600

1,800
51

Fall-, Late Fall-, and Spring-Run Distribution and Relative Abundance

We captured juvenile fall-, late fall-, or spring-run Chinook Salmon in nearly all seine regions 

and trawl sites during the 2012 and 2013 field seasons (Tables A.3 and A.4). Until the 2000 field 

season, hatchery fish were often released in groups within the watershed that did not have any 

marked individuals containing a CWT (Kevin Niemela, USFWS, personal communication; 

PSMFC 2014). As a result, we were unable to determine the origin of large numbers of fish 

captured at the Chipps Island and Sacramento trawl sites prior to the 2000 field season. 

At the Chipps Island Trawl Site, juvenile fall-, late fall-, or spring-run Chinook Salmon were

generally captured during December through July during both field seasons (Figure 25).

Individuals were generally captured from January through June at the Sacramento Trawl Site, but 

some individuals were observed as early as November during the 2013 field season 

corresponding to increased discharge (Figure 26). In general, we observed a greater proportion of 

hatchery fish (estimated and marked) relative to natural fish during this period at the Chipps 

Island and Sacramento trawl sites based on hatchery releases upstream of these locations. The 

majority of fish captured at the Mossdale Trawl Site that occurred between March and June were 

considered to be natural origin due to few hatchery releases occurring in the San Joaquin Basin 

(PSMFC 2014; Figure 27). At all the trawl sites, the peak-mean monthly CPUE representing 

natural individuals occurred in April and May during both field seasons. The mean yearly CPUE

at the Chipps Island Trawl Site has declined annually since the 2011 field season, however the 

2012 and 2013 CPUEs exceeded or were equal to their historical averages (Figures 25 and 28). 

This assumes that catch efficiency at Chipps Island did not vary between 2011 (a high flow year) 

and 2012 and 2013 (low flow years; Table A.19). Conversely, the mean yearly CPUE at the 

Sacramento and Mossdale trawl sites appear to be increasing since their record low CPUE was 

observed during the 2010 field season (Figures 26 and 27). During the 2013 field season, we 

observed the record high CPUE of natural juvenile fall-, late fall-, or spring-run Chinook Salmon 

at the Mossdale Trawl Site relative to the 2004 through 2011 field seasons (Figure 27). Although 

these races are grouped for consistency within this report, juvenile Chinook Salmon captured at 

Mossdale are assumed to be fall-run.

Estimated natural juvenile fall-, late fall-, or spring-run Chinook Salmon were generally captured 

using beach seines between December and May during the 2012 and 2013 field seasons (Figure 

29). We observed few marked fish during both field seasons. The mean monthly CPUE of 

natural fall-, late fall-, or spring-run Chinook Salmon peaked in the Lower Sacramento River and 

North Delta seine regions during January and February. The mean yearly CPUE estimates 

suggested that natural juvenile fall-, late fall-, or spring-run Chinook Salmon were consistently 

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

and to a lesser extent the Central Delta seine regions, relative to other seine regions since the 

2000 field season (Figure 30).
52

Figure 25. The mean monthly and yearly CPUE (bars) of juvenile fall-, late fall-, and spring-run

Chinook Salmon captured in MWTRs at the Chipps Island Trawl Site, and the estimated mean 

monthly and yearly Delta outflow (solid line) during the (A) 2012, (B) 2013, and (C) 1995 

through 2013 field seasons. 

(C) 1995–2013 field seasons 

Mean discharge (m

3/sec)

1,200

1,400

1,600

1,800

1,200

1,400

1,600

1,800

1,200

1,400

1,600

1,800

1,000

1,000

1,000
53

Figure 26.The mean monthly and yearly CPUE (bars) of juvenile fall-, late fall-, and spring-run

Chinook Salmon captured in MWTRs (solid bars) and KDTRs (striped bars) at the Sacramento 

Trawl Site, and the mean monthly and yearly Sacramento River discharge at Freeport (solid line) 

during the (A) 2012, (B) 2013, and (C) 2000 through 2013 field seasons. 

(C) 2000–2013 field seasons 

Mean discharge (m

3/sec)

1,000

1,200

1,400

1,000

1,200

1,400

1,000

1,200

1,400
54

Figure 27. The mean monthly and yearly CPUE (bars) of juvenile fall-, late fall-, and spring-run

Chinook Salmon captured in KDTRs at the Mossdale Trawl Site, and the mean monthly and 

yearly San Joaquin River discharge at Vernalis (solid line) during the (A) 2012, (B) 2013, and 

(C) 2004 through 2013 field seasons. Juvenile Chinook Salmon captured at Mossdale are 

assumed to be fall-run only.

(C) 2004–2013 field seasons 

Mean discharge (m

3/sec)
55

Figure 28. The mean monthly and yearly CPUE (bars) of juvenile fall-, late fall-, and spring-run Chinook Salmon captured in MWTRs 

at the Chipps Island Trawl Site, and the estimated mean monthly and yearly Delta outflow (solid line) during April–June of the 1978–

2013 field seasons.

Mean discharge (m

3

1,000

/sec)

2,000

2,500

3,000

1,500
56

Figure 29. The mean monthly CPUE (bars) of juvenile fall-, late fall-, and spring-run Chinook Salmon captured within the Lower 

Sacramento River (1), North Delta (2), Central Delta (3), South Delta (4), Lower San Joaquin River (5), and San Francisco and San 

Pablo Bay (6) beach seine regions, and the estimated mean monthly and yearly Delta outflow (dashed line), Sacramento River 

discharge at Freeport (solid line), and San Joaquin River discharge at Vernalis (dotted line) during the (A) 2012 and (B) 2013 field 

seasons.

Mean discharge (m

3/sec)

12,000

10,000

8,000

6,000

4,000

2,000

12,000

10,000

8,000

6,000

4,000

2,000

CPUE (fish/10,000 m3)

1,200

1,400

1,000

1,200

1,400

1,000

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

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

1 23 4 56 1 23 4 56 1 23 4 56 1 23 4 56 1 23 4 56 1 23 4 56

1 23 4 56 1 23 4 56 1 23 4 56 1 23 4 56 123 4 56 1 23 4 56 1 23 4 56 1 23 4 56 1 23 4 56 1 23 4 56 1 23 4 56 1 23 4 56

1 23 4 56 1 23 4 56 1 23 4 56 1 23 4 56 1 23 4 56 1 23 4 56
57

Figure 30. The mean yearly CPUE (bars) of juvenile fall-, late fall-, and spring-run Chinook Salmon captured within the Lower 

Sacramento River (1), North Delta (2), Central Delta (3), South Delta (4), Lower San Joaquin River (5), and San Francisco and San 

Pablo Bay (6) beach seine regions, and the estimated mean monthly and yearly Delta outflow (dashed line), Sacramento River 

discharge at Freeport (solid line), and San Joaquin River discharge at Vernalis (dotted line) during the 2000 through 2013 field 

seasons. 

Mean discharge (m

3/sec)

1,000

2,000

3,000

4,000

5,000

6,000

7,000

1,000

1,200

1,400

1,600

1,800

123456 123456 123456 123456 123456 123456 123456 123456 123456 123456 123456 123456 123456 123456
58

Absolute Abundance

Among the 102 release groups used to estimate the TRR ̅̅̅̅̅̅ at the Chipps Island Trawl Site, 

9,670,244 fish were marked with a CWT (PSMFC 2014). Release groups ranged in size from 

22,911 to 717,966 individuals. The TRR ̅̅̅̅̅̅ at the Chipps Island Trawl Site was estimated to be 

0.48% ± 0.08% (mean ± 95% CI), using CWT recoveries from 1989 to 2013. The duration of 

recoveries of CWT fish within a release group spanned, on average, 11.5 days.

We used 42 release groups to estimate the TRR ̅̅̅̅̅̅ of the MWTR at the Sacramento Trawl Site.

Within these release groups, 2,398,810 fish were marked with a CWT. Release groups ranged in 

size from 34,480 to 104,516 individuals. The duration of recoveries of CWT fish within a release 

group spanned, on average, 10.8 days. Two of the release groups did not have any individuals 

captured at the site. The TRR ̅̅̅̅̅̅ of the MWTR was estimated to be 0.82% ± 0.35%, using CWT 

releases from 1988 to 2009. We used 5 release groups to estimate the TRR ̅̅̅̅̅̅ of the KDTR at the 

Sacramento Trawl Site, where a total of 300,960 fish were marked with a CWT (PSMFC 2014). 

Release groups ranged in size from 48,987 to 69,490 individuals. The duration of recoveries of 

CWT fish within a release group spanned, on average, 4.9 days. The TRR ̅̅̅̅̅̅ of the KDTR was 

estimated to be 0.74% ± 0.87% between 1996 and 2006.

There were 53 release groups used to estimate the TRR ̅̅̅̅̅̅ at the Mossdale Trawl Site. Among these 

release groups, 438,529 individuals were marked either with stain dye (Steve Tsao, CDFW, 

personal communication) or an adipose fin clip and contained a CWT (PSMFC 2014). Release 

groups ranged in size from 1,195 to 74,411 individuals. The TRR ̅̅̅̅̅̅ was estimated to be 2.88% ±

3.00%, using CWT and stain dye releases from 1997 to 2013. The duration of recoveries of 

marked fish within a release group spanned, on average, 1 day. Six of the release groups did not 

have any recoveries. While the T̅̅̅RR̅̅̅ rate for the CWT groups (0.64% ± 0.83%) was comparable 

with the estimate for the Chipps Island and Sacramento trawl sites (0.48% ± 0.08% and 0.82% ±

0.35%, respectively; see above), the TRR ̅̅̅̅̅̅ of the stain dye groups were considerably higher 

(6.52% ± 4.93%). The increased recoveries may be due to unintentional targeting of marked fish 

or a time effect. In general, CWT releases occurred at random relative to sampling at the 

Mossdale Trawl Site, whereas spray dye fish were released at the beginning of a sample day 

(SJRGA 2009). 

The TRR ̅̅̅̅̅̅ had a negative lower 95% confidence limit for both the Sacramento Trawl Site 

(KDTR) and the Mossdale Trawl Site, which is due to relatively small sample sizes coupled with 

considerable variation among samples. Because a negative or zero value of T̅̅̅RR̅̅̅ results in an 

absolute abundance of infinity, and the lower TRR ̅̅̅̅̅̅ confidence limit was used to estimate the 

upper absolute abundance confidence limit, we assigned the lower TRR ̅̅̅̅̅̅ confidence limit as

0.10% in order to provide absolute abundance confidence limits. This value was chosen based on 

a conservative comparison to the lower TRR ̅̅̅̅̅̅ confidence limits at the Chipps Island and 

Sacramento (MWTR) trawl sites (0.40% and 0.47%, respectively; see above). We highly 

recommend further investigation of the efficiency of each of the trawls to obtain more precise 

and accurate absolute abundance estimates that can be used to inform future management 

decisions within the San Francisco Estuary and its watershed. 
59

We estimated, on average, a total of 107,224 (68% natural origin, 32% marked) and 208,658

(99% natural origin, 1% marked) juvenile winter-run sized Chinook Salmon immigrating into the 

Delta at the Sacramento Trawl Site during the 2012 and 2013 field seasons, respectively (Figure 

31). However, a total of 292,903 (84% natural origin, 16% marked) and 217,001 (99% natural,

origin, 1% marked) juvenile winter-run sized Chinook Salmon were estimated to emigrate from 

the Delta at Chipps Island during the 2012 and 2013 field seasons, respectively (Figure 32). 

Since we estimated that more winter-run sized Chinook Salmon exited the Delta than entered the 

Delta in 2012, no reproduction of winter-run Chinook Salmon can occur in the Delta, and no 

hatchery releases of winter-run Chinook Salmon were made downstream of the Sacramento 

Trawl Site; we believe that either the absolute abundance of winter-run Chinook Salmon at 

Chipps Island is over-estimated or the absolute abundance at the Sacramento Trawl Site is underestimated. It might be more likely that the absolute abundance at Chipps Island is over-estimated, 

since the river LDC has been shown to over-estimate a higher number of genetic winter-run at 

Chipps Island than at the Sacramento Trawl Site (Dekar et al. 2013). Genetic tissue sampling 

could help us distinguish between true winter-run and winter-run sized fish in the catch and 

allow more precise and accurate estimates of winter-run abundance at the Sacramento and 

Chipps Island trawl sites. Regardless, it is apparent that the abundance of winter-run Chinook 

Salmon at Chipps Island is highly variable and has declined considerably since the 1990s (Figure 

32). 

The mean yearly absolute abundance of all juvenile fall-, late fall-, and spring-run Chinook 

Salmon immigrating into the Delta was estimated to be 7,736,290 and 9,688,494 individuals 

during the 2012 and 2013 field seasons, respectively (Figures 33 and 34). We estimated, on 

average, a total of 6,254,907 (62% natural origin, 24% hatchery origin, 14% marked) and 

7,626,927 (52% natural origin, 28% hatchery origin, 19% marked) juveniles at the Sacramento 

Trawl Site during the 2012 and 2013 field seasons (Figure 33). Additionally, 1,481,383 (72% 

natural origin, 28% marked) and 2,061,567 (97% natural origin, 2% hatchery origin, 1% marked) 

juveniles were estimated at the Mossdale Trawl Site during the 2012 and 2013 field seasons 

(Figure 34). At the Chipps Island Trawl Site, we estimated a total of 13,404,233 (43% natural 

origin, 37% hatchery origin, 21% marked) and 11,095,289 (33% natural origin, 43% hatchery 

origin, 23% marked) juveniles emigrating from the Delta during the 2012 and 2013 field seasons 

(Figure 35). 

Although inter-annual trends in abundance at the Sacramento and Mossdale trawl sites are 

difficult to discern due to the high uncertainty, it is apparent that the abundance of juvenile fall-, 

late fall-, and spring-run Chinook Salmon has declined considerably at the Chipps Island Trawl 

Site relative to the 1990s (Figure 35). The absolute abundance of juvenile fall-, late fall-, or 

spring-run Chinook Salmon at Chipps Island increased in 2012 relative to the 2010 and 2011 

field seasons, and in 2013 remained similar to the 2010 and 2011 field seasons (Speegle et al. 

2013). While there was increased adult escapement in both 2012 and 2013 (Table A.22), the 

decrease in absolute abundance at Chipps Island during the 2013 field season may be partly due 

to the worsening drought conditions in 2013 (Swain et al. 2014; Table A.19).

The absolute abundance estimates for juvenile Chinook Salmon presented in this report likely 

contain bias from several sources, in addition to potentially inaccurate race designations caused 

by the application of the LDC. Firstly, we assumed that unmarked individuals were never 
60

recaptured. This assumption was violated based on the capture of five CWT individuals in 2012 

and four CWT individuals in 2013 that were released downstream of Chipps Island (San Pablo 

Bay) by the Chipps Island MWTR (Tables A.20 and A.21). Therefore, our abundance estimates 

may be over-estimated to an unknown degree. Secondly, we may have under-estimated the 

absolute abundance of juvenile Chinook Salmon at each of the trawl sites due to the possible size 

selectivity of the MWTR’s and KDTR’s cod end design and mesh. Thirdly, we assumed that 

juvenile Chinook Salmon were equally distributed in time, which is unlikely due to diel 

migratory patterns. Several studies have shown primarily nocturnal migratory behavior in 

juvenile Chinook Salmon (Gaines and Martin 2002; Williams 2006 and references therein), 

while some studies in the Delta have provided evidence for diurnal migration of juvenile 

Chinook Salmon during the spring (Buchanan 2014; Wilder and Ingram 2006). While Bradford 

and Higgins (2001) mostly observed nocturnal activity, additional observations of a variety of 

diel activity patterns in the Bridge River of British Columbia led them to conclude that diel 

activity is caused by individual fish responding to fine-scale habitat attributes and is difficult to 

generalize. Given that the DJFMP only samples during the day, any diel activity patterns of 

juvenile Chinook Salmon could produce an unknown effect on the estimate of absolute 

abundance at all sampling locations. More investigation is needed to understand the effect of diel 

migratory patterns of juvenile Chinook Salmon on catch efficiency. 
61

Figure 31. Mean absolute abundance estimates and their 95% confidence intervals for juvenile winter-run Chinook Salmon at the 

Sacramento Trawl Site when (A) MWTRs (solid bars) and (B) KDTRs (striped bars) were used during the 2000–2013 field seasons. 

The y-axis is presented on a common log scale.

1

10

100

1,000

10,000

100,000

1,000,000

10,000,000

2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013

(A) MWTR

1

10

100

1,000

10,000

100,000

1,000,000

10,000,000

2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013

(B) KDTR

Absolute abundance (log)

Estimated natural origin

Estimated hatchery origin

Marked
62

Figure 32. Mean absolute abundance estimates and their 95% confidence intervals for juvenile winter-run Chinook Salmon at the 

Chipps Island Trawl Site during the 1995–2013 field seasons. Years with asterisks indicate that 1 or 2 months of that field season were 

not sampled, which may bias low the annual estimate.

0

200,000

400,000

600,000

800,000

1,000,000

1,200,000

1995* 1996 1997* 1998* 1999 2000 2001 2002 2003 2004 2005 2006 2007* 2008* 2009 2010 2011 2012 2013

Absolute abundance

Estimated natural origin

Estimated hatchery origin

Marked
63

Figure 33. Mean absolute abundance estimates and their 95% confidence intervals for juvenile fall-, late fall-, and spring-run Chinook 

Salmon at the Sacramento Trawl Site when (A) MWTRs (solid bars) and (B) KDTRs (striped bars) were used during the 2000–2013 

field seasons. The y-axis is presented on a common log scale.

1

10

100

1,000

10,000

100,000

1,000,000

10,000,000

100,000,000

1,000,000,000

2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013

(A) MWTR

1

10

100

1,000

10,000

100,000

1,000,000

10,000,000

100,000,000

1,000,000,000

2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013

(B) KDTR

Absolute abundance (log)

Estimated natural origin

Estimated hatchery origin

Marked

Unknown
64

Figure 34. Mean absolute abundance estimates and their 95% confidence intervals for juvenile fall-, late fall-, and spring-run Chinook 

Salmon at the Mossdale Trawl Site during the 2004–2013 field seasons. The y-axis is presented on a common log scale. Juvenile 

Chinook Salmon captured at Mossdale are assumed to be fall-run only.

1

10

100

1,000

10,000

100,000

1,000,000

10,000,000

100,000,000

2004 2005 2006 2007 2008 2009 2010 2011 2012 2013

Estimated natural origin

Estimated hatchery origin

Marked

Unknown

Absolute abundance (log)
65

–

Figure 35. Mean absolute abundance estimates and their 95% confidence intervals for juvenile fall-, late fall-, and spring-run Chinook 

Salmon at the Chipps Island Trawl Site (A) during April–June during the 1978–2013 field seasons and (B) year-round during the 

1995–2013 field seasons. Years with asterisks indicate that 1 or 2 months of that field season were not sampled, which may bias low 

the annual estimate. 

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

50,000,000

1995* 1996 1997* 1998* 1999 2000 2001 2002 2003 2004 2005 2006 2007* 2008* 2009 2010 2011 2012 2013

(B) 1995–2013 field seasons

0

10,000,000

20,000,000

30,000,000

40,000,000

50,000,000

60,000,000

70,000,000

19781979198019811982198319841985198619871988198919901991199219931994199519961997

1998*

19992000200120022003200420052006

2007*

200820092010201120122013

(A) April–June of 1978–2013

Absolute abundance

Estimated natural origin

Estimated hatchery origin

Marked

Unknown
66

Fork Length Distributions

Unmarked juvenile Chinook Salmon varied considerably in size between seine regions and trawl 

sites during the 2012 and 2013 field seasons (Figures 36–40). However, there were only weak 

inter-annual differences in FLs within beach seine regions and trawl sites between the 2012 and 

2013 field seasons. The majority of fishes were identified as fry (FL<70 mm; Kjelson et al. 

1982) and individuals were slightly larger (1–6 mm FL) within most seine regions and trawl sites 

during the 2012 field season. The 2012 field season was wetter compared to the 2013 field 

season, but both field seasons occurred during below normal, dry, and critically dry water years

(Table A.19). The FL distribution of unmarked juvenile Chinook Salmon captured during both 

the 2012 and 2013 field seasons ranged from 60–140 mm using the MWTR at the Chipps Island 

Trawl Site (Figure 36). At the Mossdale Trawl Site, the FL of fish captured by the KDTR ranged 

from 60–110 mm (Figure 36). Fish captured by the KDTR and MWTR at the Sacramento Trawl 

Site ranged from 30–65 mm and 60–100 mm (FL), respectively (Figure 37). For beach seines, 

the range was 26‒111 mm in 2012 and 26‒199 mm during the 2013 field season (Figures 38–

40). In contrast to beach seine catches, the majority of fishes captured by MWTR 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 are largely 

consistent with the observations made during the 2010 and 2011 field seasons (Speegle et al. 

2013) and 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 nets (i.e., Chipps Island=MWTR, Mossdale=KDTR, and Sacramento=KDTR and

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 considering 

determining if and how gear efficiency varies among gear types, methods, and locations. 
67 0 50 100 150 200

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(A) Chipps Island Trawl Site

2012 field season

(B) Chipps Island Trawl Site

2013 field season

(C) Mossdale Trawl Site

2012 field season

(D) Mossdale Trawl Site

2013 field season

Figure 36. Fork length distributions for juvenile Chinook Salmon captured in MWTRs at the

Chipps Island Trawl Site and KDTRs at the Mossdale Trawl Site during the 2012 and 2013 field 

seasons.
68

Figure 37. Fork length distributions for unmarked juvenile Chinook Salmon captured in MWTRs 

and KDTRs at the Sacramento Trawl Site during the 2012 and 2013 field seasons.

0 50 100 150 200

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80

100

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2012 field season

(B) Sacramento Trawl Site (MWTR)

2013 field season

(C) Sacramento Trawl Site (KDTR)

2012 field season

(D) Sacramento Trawl Site (KDTR)

2013 field season
69

Figure 38. Fork length distributions for unmarked juvenile Chinook Salmon captured in beach 

seines within the Lower Sacramento River (Region 1) and North Delta (Region 2) beach seine 

regions during the 2012 and 2013 field seasons.

0 20 40 60 80 100 120 140

0

50

100

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200

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300

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2012 field season

(B) Region 1

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(D) Region 2

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70 0 20 40 60 80 100 120 140

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3

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2012 field season

(B) Region 3

2013 field season

(C) Region 4

2012 field season

(D) Region 4

2013 field season

Figure 39. Fork length distributions for unmarked juvenile Chinook Salmon captured in beach 

seines within the Central Delta (Region 3) and South Delta (Region 4) beach seine regions 

during the 2012 and 2013 field seasons.
71

Figure 40. Fork length distributions for unmarked juvenile Chinook Salmon captured in beach 

seines within the Lower San Joaquin River (Region 5) and San Francisco and San Pablo Bay 

(Region 6) beach seine regions during the 2012 and 2013 field seasons.

0 20 40 60 80 100 120 140

0

1

2

3

0 20 40 60 80 100 120 140

0

1

2

3

4

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0 20 40 60 80 100 120 140

0

1

2

(A) Region 5

2012 field season

(B) Region 5

2013 field season

(C) Region 6

2012 field season

(D) Region 6

2013 field season
72

MONITORING FOR DELTA CROSS CHANNEL OPERATIONS

Introduction

The DCC was constructed by the U.S. Bureau of Reclamation (USBR) in 1951 at Walnut Grove, 

California. The DCC was designed to facilitate the transfer of fresh water from the Sacramento 

River southwards through the channels of the Mokelumne River system towards the south Delta. 

Ultimately, water is diverted to the CVP and SWP pumps at Tracy which provide water for 

agricultural, municipal, and industrial uses within the Central Valley and southern California. 

The DCC gates enable USBR operators to prevent mixing of Sacramento River water with the 

more saline water in the western Delta prior to export. Before 1978, the DCC gates remained 

open, except during periods of high Sacramento River flow (20,000 to 25,000 cfs) when risks of 

channel scouring or downstream flooding warranted their closure. The USBR currently operates 

the DCC gates in the open position to (1) improve the transfer of water from the Sacramento 

River to the CVP and SWP pumping facilities, (2) improve water quality in the southern Delta, 

and (3) reduce saltwater intrusion rates in the western Delta.

The operation of the DCC gates alters tidal and river flows throughout the Estuary and thereby 

influences the migration pathways and survival of emigrating juvenile Chinook Salmon (Kjelson 

and Brandes 1989; Kimmerer 2008; Newman and Brandes 2010; Perry et al. 2010). Both the 

Federal ESA-listed spring-run and winter-run juvenile Chinook Salmon can be diverted into the 

central Delta when the DCC gates are open. In the central Delta, juvenile Chinook Salmon may 

experience lower survival rates due to water export, high temperatures, predation, and pollution 

(Moyle 1994; Brandes and McLain 2001; Kimmerer 2008; Newman and Brandes 2010). 

Because ESA-listed species, including spring-run and winter-run Chinook Salmon, are affected 

by DCC operations, attempts have been made by state and federal agencies to reduce their entry 

into the central Delta. 

In 1978, the State Water Resources Control Board (SWRCB) instituted a decision (D-1485) to 

amend the water right permits of the CDWR and USBR for the SWP and the CVP facilities, 

respectively (SWRCB 1978). This decision mandated that in addition to reducing direct water 

diversion at the project pumps and releasing stored or natural water flows, DCC gate operations 

could be used to ensure adequate river flow for salinity control and to improve water quality for 

fish and wildlife in the estuarine ecosystem. The 1995 Water Quality Control Plan (WQCP) for 

the San Francisco Estuary (95-1) included specific guidelines for the operation of the DCC gates 

for the protection of threatened or endangered fish (SWRCB 1995), which were reaffirmed by 

the SWRCB in 1999 (D-1641) and the 2006 WQCP for the San Francisco Estuary (SWRCB 

2006). Recovery and protection plans for juvenile winter-run and spring-run Chinook Salmon 

were the basis for the salmon decision processes in controlling DCC gate operations for the 

protection of ESA-listed species (NMFS 1997, 2009b). 

Further modifications of DCC gate operations were instituted through the 2009 NMFS RPA, 

with 2011 amendments (NMFS 2011) that resulted from 2010 independent review panel report 

(Anderson et al. 2010). The current DCC operation plan (NMFS 2011, Action IV.1.2) mandates 

that the DCC gates be closed from October through November if fish are present. Contingent 

upon water quality conditions, the DCC gates remain closed from December through January 
73

except during experiments approved by NMFS investigating fish migration patterns occurring 

from December 1 through December 14 (Table 2). The NMFS RPA mandates DCC closures 

from February 1 to May 20 and from May 21 to June 15 if needed (NMFS 2011).

To facilitate coordination among the fishery resource agencies and project operators, a salmon 

decision process (refer to NMFS 2011 for the current process, Action IV.1.2) was drafted to 

minimize the impact of the DCC on emigrating salmonids and Green Sturgeon Acipenser

medirostris. Once the salmon decision process is triggered, depending on the magnitude of the 

catch and the water quality, recommendations are made to USBR through the Delta Operations 

for Salmonids and Sturgeon group (DOSS) to close the DCC gates (Table 2). The DOSS group is 

a technical advisory group made up of NMFS, USFWS, CDWR, CDFW and USBR (NMFS 

2011, Action IV.5). The Knights Landing Catch Index (KLCI) and the Sacramento Catch Index 

(SCI) are the criteria upon which the first action is based for closing the DCC gates. The KLCI is 

calculated using catch data from the CDFW rotary screw trap located at Knights Landing. The 

SCI is generated from beach seine and trawl catch data collected by the DJFMP on the 

Sacramento River.

The catch data are provided to the DOSS group through the Data Assessment Team (DAT) 

report. The SCI, used alone or in conjunction with the KLCI or increases in the average daily 

flow rates, may trigger various actions of the modified Chinook Salmon decision process (Table 

2). In this section of the report, we will discuss how the relative abundance indices of unmarked 

winter-run sized or older juvenile Chinook Salmon occurring near Sacramento informed realtime DCC water operation decisions.

Methods

The SCI was calculated using unmarked juvenile Chinook Salmon catch data collected either at 

the Sacramento Trawl Site or within the Sacramento Area Seine Region (Table 1; Figure 41). In 

general, the Sacramento Trawl Site was sampled three days per week from October through 

January during the 2012 and 2013 field seasons. In addition, eight beach seine sites located 

within the Sacramento Area Seine Region were sampled three days per week from October 

through December and one day per week in January (Tables A.23 and A.24). The increased 

sampling frequency using beach seines during October through December was intended to better 

detect winter-run sized or older juvenile Chinook Salmon migrating near the DCC and inform 

real-time water diversion decisions (NMFS 2011). Although the frequency of sampling at the 

Sacramento Trawl Site was not increased during this period, the Sacramento trawl did use a 

larger KDTR in place of the MWTR to sample larger juvenile Chinook Salmon. The sampling 

methodologies and fish processing methods were the same as described earlier within the “LongTerm Monitoring” section. The race of all unmarked juvenile Chinook Salmon was categorized

using the river LDC developed by Fisher (1992) and modified by Greene (1992).
74

Table 2. The Salmon Decision Process (NMFS 2011, RPA Action IV.1).

Time Trigger Action

Oct 1–Nov 30 Water quality criteria met, Knights Landing Catch Index 

(KLCI) and/or Sacramento Catch Index (SCI) > 3 and ≤ 5

Close Delta Cross Channel (DCC) gates for 3 days

 within 24 hours

Water quality criteria met, KLCI and/or SCI > 5 Close DCC gates until index < 3

Water quality criteria not met, KLCI and/or SCI > 3 DOSS elevates decision to NMFS & Water

 Operations Management Team (WOMT)

Dec 1–Dec 14 Water quality criteria are met DCC gates closed, may be opened for Delta Action 8

Water quality criteria not met, and KLCI and/or SCI < 3 Open DCC gates until water quality criteria met

Water quality criteria not met, and KLCI and/or SCI > 3 DOSS elevates decision to NMFS & WOMT

Dec 15–Jan 31 No triggers needed DCC gates closed

NMFS-approved experiments conducted DCC gates may be opened for 5 days

Feb 1–May 20 D-1641 mandatory gate closure DCC gates closed per water quality criteria

May 21–Jun 15 D-1641 gate operations criteria DCC gates closed for 14 days, if NMFS warrants
75

Figure 41. Delta Cross Channel sites sampled during the 2012 and 2013 field season within the 

lower Sacramento and San Joaquin rivers and San Francisco Estuary. 
76

The SCI represents the number of winter-run size or larger juvenile Chinook Salmon captured 

within a day at the Sacramento Trawl Site or within the Sacramento Area Seine Region 

standardized to one day of effort and is calculated as:

SCIdG =

∑ CatchdG

SamplesdG

· SEG

(8)

Where d indexes a sample day, G indexes gear type (i.e., seine or trawl), CatchdG represents the 

number of winter-run sized or larger juvenile Chinook Sample captured using gear type G during 

sample day d, SamplesdG represents the number of seine hauls or trawl tows completed during 

sample day d using gear type G, and SEG represents the standard number of samples completed 

using gear type G during a typical sample day (SEseine=8 and SEtrawl=10). All samples regardless 

of their condition (e.g., good, poor, etc.) were used for SCI estimates for each sample day. 

Results and Discussion

Unmarked winter-run sized or larger juvenile Chinook Salmon were first detected within the 

Sacramento Area Beach Seine Region near the DCC water diversion gates during the months of 

October and November for the 2012 and 2013 field seasons respectively (Figure 42). The 

DJFMP Sacramento Catch Index did not trigger any DCC operations in the 2012 field season.

However, the Sacramento Trawl SCI or the Sacramento Beach Seine SCI exceeded the threshold 

of the salmon decision process on 13 sampling dates during the 2013 field season (Table 3; 

Figure 42). This either triggered or maintained the closure of the DCC gates in conjunction with 

the KLCI and water quality indices on 12 occasions (DCC operational logs and final DOSS 

notes; Edmund Yu, CDWR, personal communication).

In general, the 2012 and 2013 monitoring conducted at the Sacramento Trawl Site and within the 

Sacramento Area Beach Seine Region was used to inform real-time water operations at the DCC

water diversion gates. The monitoring likely prevented ESA-listed juvenile Chinook Salmon 

diversions into the Central Delta and maximized flexibility in water operations. To improve the 

monitoring and our understanding regarding the true occupancy of winter-run sized or larger 

juvenile Chinook Salmon near the DCC, we recommend a thorough investigation of the gear 

efficiency. Knowing the gear efficiency will assist to inform real-time water operation decisions 

more effectively and efficiently. 
77

Table 3. Salmon Decision Process trigger events (Sacramento Catch Index=SCI, Knights 

Landing Catch Index=KLCI) by sample day and gear type (beach seine or trawl) during the 2012 

and 2013 field seasons.

Sample 

date

SCI

(beach 

seine)

SCI

(trawl) Action

11/21/2012 3.43 SCI would have triggered closure had index been calculated

11/23/2012 6.86 9.00 All three indices triggered (KLCI, SCIs), gates closed on 11/27

11/24/2012

11/25/2012

11/26/2012 16.00 44.00 All three indices triggered (KLCI, SCIs), gates closed on 11/27

11/27/2012

11/28/2012 17.14 KLCI triggered on 11/27, SCI kept gates closed until 11/30

12/01/2012 17.60 SCI maintained closure until 12/14

12/02/2012

12/03/2012 40.00 25.00 SCI maintained closure until 12/14

12/04/2012 48.00 SCI maintained closure until 12/14

12/05/2012

12/06/2012 14.40 SCI maintained closure until 12/14

12/07/2012 24.00 9.23 SCI maintained closure until 12/14

12/08/2012

12/09/2012

12/10/2012 42.67 SCI maintained closure until 12/14

12/11/2012

12/12/2012 20.57 SCI maintained closure until 12/14

12/13/2012 8.00 SCI maintained closure until 12/14

12/14/2012 4.57 SCI maintained closure until 12/14
78

(A) 2012 field season

Oct Nov Dec Jan Feb 

0

10

20

30

40

50

(B) 2013 field season

Oct Nov Dec Jan Feb 

Catch indices

0

10

20

30

40

50

Seine SCI 

Trawl SCI 

Min trigger

Max trigger

Figure 42. Sacramento Catch Index (SCI) estimates generated by the catch of winter-run size or 

larger juvenile Chinook Salmon in the Sacramento Trawl Site and within the Sacramento Area 

Beach Seine Region during the (A) 2012 and (B) 2013 field seasons and the minimum (blue 

dashed line) and maximum (red dashed line) SCI values required to trigger recommendations to 

close the Delta Cross Channel gates.

↑

Dec 14

↑

Dec 14
79

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84

APPENDIX
85

Table A.1. Sites sampled during the 2012 and 2013 field seasons 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

Coordinates (UTM) 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 Knights Landing Yolo 10 S 4295506 610842 1981

SR080Ea VeronaaSutter 10 S 4293731 620049 1981

SR071EaElkhornaSacramento 10 S 4281359 619626 1981

Region 2: North Delta Seine

SR060Eb Discovery ParkbSacramento 10 S 4273503 629820 1976

AM001Sb American RiverbSacramento 10 S 4273377 630121 1976

SR049Eb Garcia BendbSacramento 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
86

Table A.1. Continued.

Site code Site name County

Coordinates (UTM) 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

SJ083Wc N. of Tuolumne RivercStanislaus 10 S 4164462 660960 1994

SJ077E c Route 132cStanislaus 10 S 4167222 656395 1994

SJ074W cSturgeon BendcSan Joaquin 10 S 4170903 654784 1994

SJ068W c Durham SitecSan Joaquin 10 S 4173594 652327 1994

SJ063W c Big BeachcSan Joaquin 10 S 4176666 650093 1994

SJ058Wd WeatherbeedSan Joaquin 10 S 4181923 649451 1994

SJ056Ed MossdaledSan Joaquin 10 S 4183536 649043 1994

SJ079Ee San Luis Refugee

Stanislaus 10 S 4166449 657914 2008

SJ076We N. of Route 132e

Stanislaus 10 S 4168198 656679 2008

SJ074Ae Sturgeon Bend 

Alternatee 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
87

Table A.1. Continued.

Site code Site name County

Coordinates (UTM) 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

a

Site was included within both Region 1 and Region 7 from Oct 1 to Jan 31.

b

Site was included within both Region 2 and Region 7 from Oct 1 to Jan 31.

c Site was sampled when San Joaquin River discharge was > 51m3/s during the 2000–2012

field seasons, and year-round during the 2013 field season.

d

Site was sampled throughout the field season during 2000–2013.

e

Site was sampled when San Joaquin River discharge was ≤ 51m3/s during the 2000–2012

field seasons.
88

Table A.2. Fish species, common names, and assemblage groups. Fish species are listed in 

phylogenetic order.

Common name Genus Species Assemblage group

River Lamprey Lampetra ayresii Anadromous-benthic-native

Western Brook Lamprey Lampetra richardsoni Benthic-native

Pacific Lamprey Lampetra tridentatus Anadromous-benthic-native

Spiny Dogfish Squalus acanthias Benthic-native

Gray Smoothhound Mustelus californicus Benthic-native

Brown Smoothhound Mustelus henlei Benthic-native

Leopard Shark Triakis semifasciata Benthic-native

Pacific Electric Ray Torpedo californica Benthic-native

Thornback Ray Platyrhinoidis triseriata Benthic-native

Big Skate Raja binoculata Benthic-native

Bat Ray Myliobatis californica Benthic-native

Green Sturgeon Acipenser medirostris Anadromous-benthic-native

White Sturgeon Acipenser transmontanus Anadromous-benthic-native

American Eel Anguilla rostrata Benthic-nonnative

Northern Anchovy Engraulis mordax Pelagic-native

American Shad Alosa sapidissima Anadromous-pelagicnonnative

Pacific Herring Clupea pallasii Pelagic-native

Threadfin Shad Dorosoma petenense Pelagic-nonnative

Pacific Sardine Sardinops sagax Pelagic-native

Goldfish Carassius auratus Pelagic-nonnative

Red Shiner Cyprinella lutrensis Pelagic-nonnative

Common Carp Cyprinus carpio Benthic-nonnative

Tui Chub Gila bicolor Pelagic-native

California Roach Hesperoleucus symmetricus Pelagic-native

Hitch Lavinia exilicauda Pelagic-native

Hardhead Mylopharodon conocephalus Pelagic-native

Golden Shiner Notemigonus crysoleucas Pelagic-nonnative

Sacramento Blackfish Orthodon microlepidotus Pelagic-native

Rosyface Shiner Notropis rubellus Pelagic-nonnative

Fathead Minnow Pimephales promelas Pelagic-nonnative

Sacramento Splittail Pogonichthys macrolepidotus Benthic-native

Sacramento Pikeminnow Ptychocheilus grandis Pelagic-native

Speckled Dace Rhinichthys osculus Pelagic-native

Sacramento Sucker Catostomus occidentalis Benthic-native

White Catfish Ameiurus catus Benthic-nonnative

Black Bullhead Ameiurus melas Benthic-nonnative

Yellow Bullhead Ameiurus natalis Benthic-nonnative

Brown Bullhead Ameiurus nebulosus Benthic-nonnative

Blue Catfish Ictalurus furcatus Benthic-nonnative
89

Table A.2. Continued.

Common name Genus Species Assemblage group

Channel Catfish Ictalurus punctatus Benthic-nonnative

Northern Pike Esox lucius Pelagic-nonnative

Whitebait Smelt Allosmerus elongatus Pelagic-native

Wakasagi Hypomesus nipponensis Pelagic-nonnative

Surf Smelt Hypomesus pretiosus Pelagic-native

Delta Smelt Hypomesus transpacificus Anadromous-pelagic-native

Night Smelt Spirinchus starksi Pelagic-native

Longfin Smelt Spirinchus thaleichthys Anadromous-pelagic-native

Pink Salmon Oncorhynchus gorbuscha Anadromous-pelagicnonnative

Coho Salmon Oncorhynchus kisutch Anadromous-pelagic-native

Kokanee (lacustrine 

Sockeye Salmon) Oncorhynchus nerka Pelagic-nonnative

Steelhead Oncorhynchus mykiss Anadromous-pelagic-native

Chinook Salmon Oncorhynchus tshawytscha Anadromous-pelagic-native

Brown Trout Salmo trutta

Anadromous-pelagicnonnative

Plainfin Midshipman Porichthys notatus Benthic-native

Pacific Tomcod Microgadus proximus Pelagic-native

Striped Mullet Mugil cephalus Pelagic-native

Topsmelt Atherinops affinis Pelagic-native

Jacksmelt Atherinopsis californiensis Pelagic-native

Inland Silverside Menidia beryllina Pelagic-nonnative

Rainwater Killifish Lucania parva Pelagic-nonnative

Western Mosquitofish Gambusia affinis Pelagic-nonnative

Threespine Stickleback Gasterosteus aculeatus Anadromous-pelagic-native

Bay Pipefish Syngnathus leptorhynchus Pelagic-native

Brown Rockfish Sebastes auriculatus Benthic-native

Lingcod Ophiodon elongatus Benthic-native

Prickly Sculpin Cottus asper Benthic-native

Riffle Sculpin Cottus gulosus Benthic-native

Pacific Staghorn Sculpin Leptocottus armatus Benthic-native

Tidepool Sculpin Oligocottus maculosus Benthic-native

Saddleback Sculpin Oligocottus rimensis Benthic-native

Cabezon Scorpaenichthys marmoratus Benthic-native

White Bass Morone chrysops Pelagic-nonnative

Striped Bass Morone saxatilis Anadromous-pelagicnonnative

Sacramento Perch Archoplites interruptus Pelagic-native

Green Sunfish Lepomis cyanellus Pelagic-nonnative

Pumpkinseed Lepomis gibbosus Pelagic-nonnative
90

Table A.2. Continued.

Common name Genus Species Assemblage group

Warmouth Lepomis gulosus Pelagic-nonnative

Bluegill Lepomis macrochirus Pelagic-nonnative

Redear Sunfish Lepomis microlophus Pelagic-nonnative

Smallmouth Bass Micropterus dolomieu Pelagic-nonnative

Spotted Bass Micropterus punctulatus Pelagic-nonnative

Redeye Bass Micropterus coosae Pelagic-nonnative

Largemouth Bass Micropterus salmoides Pelagic-nonnative

White Crappie Pomoxis annularis Pelagic-nonnative

Black Crappie Pomoxis nigromaculatus Pelagic-nonnative

Yellow Perch Perca flavescens Pelagic-nonnative

Bigscale Logperch Percina macrolepida Pelagic-nonnative

Pacific Pompano Peprilus simillimus Pelagic-native

White Croaker Genyonemus lineatus Pelagic-native

Barred Surfperch Amphistichus argenteus Pelagic-native

Calico Surfperch Amphistichus koelzi Pelagic-native

Redtail Surfperch Amphistichus rhodoterus Pelagic-native

Kelp Perch Brachyistius frenatus Pelagic-native

Shiner Perch Cymatogaster aggregata Pelagic-native

Black Perch Embiotoca jacksoni Pelagic-native

Striped Seaperch Embiotoca lateralis Pelagic-native

Spotfin Surfperch Hyperprosopon anale Pelagic-native

Walleye Surfperch Hyperprosopon argenteum Pelagic-native

Silver Surfperch Hyperprosopon ellipticum Pelagic-native

Tule Perch Hysterocarpus traskii Pelagic-native

Dwarf Surfperch Micrometrus minimus Pelagic-native

White Seaperch Phanerodon furcatus Pelagic-native

Rubberlip Seaperch Rhacochilus toxotes Pelagic-native

Pile Perch Rhacochilus vacca Pelagic-native

Penpoint Gunnel Apodichthys flavidus Benthic-native

Saddleback Gunnel Pholis ornata Benthic-native

Red Gunnel Pholis schultzi Benthic-native

Wolf-Eel Anarrhichthys ocellatus Benthic-native

Striped Kelpfish Gibbonsia metzi Pelagic-native

Crevice Kelpfish Gibbonsia montereyensis Pelagic-native

Giant Kelpfish Heterostichus rostratus Pelagic-native

Yellowfin Goby Acanthogobius flavimanus Benthic-nonnative

Arrow Goby Clevelandia ios Benthic-native

Tidewater Goby Eucyclogobius newberryi Benthic-native

Longjaw Mudsucker Gillichthys mirabilis Benthic-native

Cheekspot Goby Ilypnus gilberti Benthic-native

Bay Goby Lepidogobius lepidus Benthic-native
91

Table A.2. Continued.

Common name Genus Species Assemblage group

Shokihaze Goby Tridentiger barbatus Benthic-nonnative

Shimofuri Goby Tridentiger bifasciatus Benthic-nonnative

Chameleon Goby Tridentiger trigonocephalus Benthic-nonnative

Pacific Sanddab Citharichthys sordidus Benthic-native

Speckled Sanddab Citharichthys stigmaeus Benthic-native

Bigmouth Sole Hippoglossina stomata Benthic-nonnative

California Halibut Paralichthys californicus Benthic-native

Pacific Halibut Hippoglossus stenolepis Benthic-native

Butter Sole Isopsetta isolepis Benthic-native

Rock Sole Lepidopsetta bilineata Benthic-native

English Sole Parophrys vetulus Benthic-native

Starry Flounder Platichthys stellatus Benthic-native

Diamond Turbot Pleuronichthys guttulatus Benthic-native

Sand Sole Psettichthys melanostictus Benthic-native
92

Table A.3. Total of individuals observed in samples used to assess the fish assemblage structure during the 2012 field season. Counts are 

grouped by species and trawl site or seine region. Fish species are listed in phylogenetic order. Beach seine regions represent sites as 

assigned in Table A.1. 

Fish species

Trawl site Beach seine region

Sacramento Mossdale Chipps 

Island 1 2 3 4 5 6

River Lamprey Lampetra ayresii 18 0 0 0 0 0 0 0 0

Pacific Lamprey Lampetra tridentatus 2 3 2 0 0 0 0 0 0

Lamprey unknown Lampetra spp. 4 0 0 1 1 1 0 0 0

Leopard Shark Triakis semifasciata 0 0 0 0 0 0 0 0 1

Bat Ray Myliobatis californica 0 0 0 0 0 0 0 0 1

White Sturgeon Acipenser transmontanus 0 0 2 0 0 0 0 0 0

Northern Anchovy Engraulis mordax 0 0 27 0 0 0 0 0 171

American Shad Alosa sapidissima 103 82 19,959 74 124 8 10 4 19

Pacific Herring Clupea pallasii 0 0 56 0 0 0 0 0 50

Threadfin Shad Dorosoma petenense 99 894 481 1,026 562 86 443 235 0

Goldfish Carassius auratus 3 4 0 11 1 0 0 20 0

Red Shiner Cyprinella lutrensis 0 286 0 716 110 1 364 5,896 0

Common Carp Cyprinus carpio 9 10 1 395 11 0 2 198 0

Hitch Lavinia exilicauda 1 1 1 101 9 4 0 4 0

Hardhead Mylopharodon conocephalus 1 33 0 36 38 0 0 0 0

Golden Shiner Notemigonus crysoleucas 24 43 2 1,292 124 62 114 58 0

Sacramento Blackfish Orthodon microlepidotus 1 2 0 63 1 0 0 9 0

Fathead Minnow Pimephales promelas 5 0 0 1,841 100 0 1 7 0

Sacramento Splittail Pogonichthys 

macrolepidotus 3 215 216 1,030 1,101 599 13 214 0

Sacramento Pikeminnow Ptychocheilus grandis 35 2 2 1,014 955 102 27 20 0

Sacramento Sucker Catostomus occidentalis 1 57 0 3,713 3,072 356 184 1,131 0

White Catfish Ameiurus catus 0 221 2 1 6 1 1 0 0

Black Bullhead Ameiurus melas 0 0 0 0 3 0 0 1 0
93

Table A.3. Continued.

Fish species

Trawl site Beach seine region

Sacramento Mossdale Chipps 

Island 1 2 3 4 5 6

Brown Bullhead Ameiurus nebulosus 0 1 0 0 0 0 3 0 0

Channel Catfish Ictalurus punctatus 10 265 0 1 1 0 0 3 0

Wakasagi Hypomesus nipponensis 20 1 2 271 728 9 0 0 0

Surf Smelt Hypomesus pretiosus 0 0 0 0 0 0 0 0 44

Delta Smelt Hypomesus transpacificus 29 0 1,160 0 63 5 0 0 0

Longfin Smelt Spirinchus thaleichthys 1 2 90 0 0 0 0 0 2

Steelhead Oncorhynchus mykiss 132 10 37 2 5 6 0 0 0

 Unmarked Steelhead 8 10 6 0 5 0 0 0 0

 Marked Steelhead 124 0 31 2 0 6 0 0 0

Juvenile Chinook Salmon Oncorhynchus 

tshawytscha 2,799 4,438 2,554 2,193 3,288 448 19 8 3

 Unmarked winter-run 29 70 45 11 11 0 1 0 0

 Unmarked fall-run 2,086 2,003 1,215 2,082 3,135 405 10 6 2

 Unmarked spring-run 258 1,149 761 76 114 41 7 1 0

 Unmarked late fall-run 1 0 0 11 12 0 0 0 0

 Unmarked not raced 0 19 0 0 0 0 0 0 0

 Marked w/ CWT 425 1,197 533 13 16 2 1 1 1

Topsmelt Atherinops affinis 0 0 8 0 0 0 0 0 5,567

Jacksmelt Atherinopsis californiensis 0 0 0 0 0 0 0 0 14

Inland Silverside Menidia beryllina 164 5,398 1 4,739 14,229 7,208 2,759 5,516 12

Rainwater Killifish Lucania parva 0 0 0 1 9 114 264 0 5

Western Mosquitofish Gambusia affinis 1 0 0 453 132 501 138 187 0

Threespine Stickleback Gasterosteus aculeatus 0 0 11 0 97 13 0 0 98

Bay Pipefish Syngnathus leptorhynchus 0 0 0 0 0 0 0 0 176

Prickly Sculpin Cottus asper 0 7 0 6 49 27 24 80 0
94

Table A.3. Continued.

Fish species

Trawl site Beach seine region

Sacramento Mossdale Chipps 

Island 1 2 3 4 5 6

Pacific Staghorn Sculpin Leptocottus armatus 0 0 1 0 22 73 2 4 147

Tidepool Sculpin Oligocottus maculosus 0 0 0 0 0 0 0 0 2

Cabezon Scorpaenichthys marmoratus 0 0 0 0 0 0 0 0 6

Striped Bass Morone saxatilis 1 878 1,185 5 143 33 27 23 33

Green Sunfish Lepomis cyanellus 0 1 0 2 4 4 26 0 0

Pumpkinseed Lepomis gibbosus 0 1 0 0 0 0 0 0 0

Warmouth Lepomis gulosus 1 0 0 0 1 4 2 0 0

Bluegill Lepomis macrochirus 5 55 3 78 100 165 440 77 0

Redear Sunfish Lepomis microlophus 1 30 1 36 151 460 1237 33 0

Smallmouth Bass Micropterus dolomieu 0 3 0 0 15 0 0 0 0

Spotted Bass Micropterus punctulatus 0 17 0 33 68 12 3 18 0

Largemouth Bass Micropterus salmoides 3 15 9 341 270 470 320 119 0

White Crappie Pomoxis annularis 0 5 0 57 2 0 0 0 0

Black Crappie Pomoxis nigromaculatus 1 9 0 214 8 3 1 65 0

Bass unknown Micropterus spp. 0 2 0 0 0 0 0 1 0

Bigscale Logperch Percina macrolepida 0 3 0 567 112 10 74 153 0

Barred Surfperch Amphistichus argenteus 0 0 0 0 0 0 0 0 37

Shiner Perch Cymatogaster aggregata 0 0 0 0 0 0 0 0 55

Black Perch Embiotoca jacksoni 0 0 0 0 0 0 0 0 4

Walleye Surfperch Hyperprosopon argenteum 0 0 0 0 0 0 0 0 21

Tule Perch Hysterocarpus traskii 0 25 14 20 445 454 19 5 0

Dwarf Surfperch Micrometrus minimus 0 0 0 0 0 0 0 0 186

White Seaperch Phanerodon furcatus 0 0 0 0 0 0 0 0 1

Pile Perch Rhacochilus vacca 0 0 0 0 0 0 0 0 2

Penpoint Gunnel Apodichthys flavidus 0 0 0 0 0 0 0 0 2
95

Table A.3. Continued.

Fish species

Trawl site Beach seine region

Sacramento Mossdale Chipps 

Island 1 2 3 4 5 6

Saddleback Gunnel Pholis ornata 0 0 0 0 0 0 0 0 1

Crevice Kelpfish Gibbonsia montereyensis 0 0 0 0 0 0 0 0 6

Yellowfin Goby Acanthogobius flavimanus 0 0 3 1 111 163 6 0 33

Arrow Goby Clevelandia ios 0 0 0 0 0 0 0 0 133

Longjaw Mudsucker Gillichthys mirabilis 0 0 0 0 0 0 0 0 1

Bay Goby Lepidogobius lepidus 0 0 0 0 0 0 0 0 21

Shokihaze Goby Tridentiger barbatus 0 0 3 0 0 0 0 0 0

Shimofuri Goby Tridentiger bifasciatus 0 0 6 0 460 31 1 0 5

Chameleon Goby Tridentiger trigonocephalus 0 0 0 0 0 0 0 0 2

Speckled Sanddab Citharichthys stigmaeus 0 0 0 0 0 0 0 0 2

California Halibut Paralichthys californicus 0 0 0 0 0 0 0 0 7

English Sole Parophrys vetulus 0 0 0 0 0 0 0 0 58

Starry Flounder Platichthys stellatus 0 0 8 0 1 2 0 0 8

Diamond Turbot Pleuronichthys guttulatus 0 0 0 0 0 0 0 0 3

Sand Sole Psettichthys melanostictus 0 0 0 0 0 0 0 0 2

Unidentified fish 0 0 0 0 0 0 0 0 1
96

Table A.4. Total of individuals observed in samples used to assess the fish assemblage structure during the 2013 field season. Counts are 

grouped by species and trawl site or seine region. Fish species are listed in phylogenetic order. Beach seine regions represent sites as assigned in 

Table A.1.

Fish species

Trawl site Beach seine region

Sacramento Mossdale Chipps 

Island 1 2 3 4 5 6

River Lamprey Lampetra ayresii 0 4 1 0 0 0 0 0 0

Pacific Lamprey Lampetra tridentatus 39 727 0 0 0 0 0 0 0

Lamprey unknown Lampetra spp. 18 5 0 0 16 0 0 0 0

White Sturgeon Acipenser transmontanus 0 0 2 0 0 0 0 0 0

Northern Anchovy Engraulis mordax 0 0 85 0 0 0 0 0 405

American Shad Alosa sapidissima 133 41 9,866 17 55 49 2 0 6

Pacific Herring Clupea pallasii 0 0 335 0 0 0 0 0 307

Threadfin Shad Dorosoma petenense 106 13,910 359 2,451 824 2,227 909 154 0

Goldfish Carassius auratus 0 0 0 0 3 0 0 0 0

Red Shiner Cyprinella lutrensis 0 89 0 685 20 1 174 13,134 0

Common Carp Cyprinus carpio 16 11 0 60 4 0 0 1 0

Hitch Lavinia exilicauda 0 1 0 23 4 0 0 1 0

Hardhead Mylopharodon conocephalus 0 1 0 64 0 0 0 1 0

Golden Shiner Notemigonus crysoleucas 5 53 1 493 36 148 93 55 0

Sacramento Blackfish Orthodon microlepidotus 0 1 0 1 0 0 0 1 0

Fathead Minnow Pimephales promelas 1 1 0 1,308 49 3 0 21 0

Sacramento Splittail Pogonichthys macrolepidotus 2 239 234 227 547 78 12 47 0

Sacramento Pikeminnow Ptychocheilus grandis 10 1 0 1,076 320 79 11 23 0

Sacramento Sucker Catostomus occidentalis 4 8 0 7,089 6,228 627 34 145 0

White Catfish Ameiurus catus 4 229 1 2 2 0 0 0 0

Black Bullhead Ameiurus melus 0 2 0 0 0 0 0 0 0

Brown Bullhead Ameiurus nebulosus 0 2 0 0 0 0 3 0 0

Channel Catfish Ictalurus punctatus 2 1,362 0 16 0 0 0 2 0
97

Table A.4. Continued.

Fish species

Trawl site Beach seine region

Sacramento Mossdale Chipps 

Island 1 2 3 4 5 6

Wakasagi Hypomesus nipponensis 11 6 4 12 19 2 0 0 1

Surf Smelt Hypomesus pretiosus 0 0 0 0 0 0 0 0 32

Delta Smelt Hypomesus transpacificus 0 0 369 0 37 89 1 0 0

Night Smelt Spirinchus starksi 0 0 1 0 0 0 0 0 0

Longfin Smelt Spirinchus thaleichthys 0 15 1,046 0 0 0 0 0 0

Steelhead Oncorhynchus mykiss 11 11 56 7 2 5 0 0 0

 Unmarked Steelhead 3 10 7 2 1 1 0 0 0

 Marked Steelhead 8 1 49 5 1 4 0 0 0

Juvenile Chinook Salmon Oncorhynchus tshawytscha 2,982 5,331 3,014 4,023 2,730 202 12 45 2

 Unmarked winter-run 74 2 65 180 98 13 0 0 0

 Unmarked fall-run 1,937 4,657 1,635 3,612 2,322 148 12 43 1

 Unmarked spring-run 392 627 600 195 278 39 0 2 1

 Unmarked late fall-run 11 0 14 5 5 0 0 0 0

 Unmarked not raced 0 0 0 0 0 0 0 0 0

 Marked w/ CWT 568 45 700 31 27 2 0 0 0

Striped Mullet Mugil cephalus 0 0 0 0 0 0 0 0 1

Topsmelt Atherinops affinis 0 0 1 0 0 0 0 0 3,693

Jacksmelt Atherinopsis californiensis 0 0 1 0 0 0 0 0 11

Inland Silverside Menidia beryllina 116 45,999 0 8,935 25,006 13,721 14,825 14,207 96

Rainwater Killifish Lucania parva 0 0 0 1 12 28 145 0 10

Western Mosquitofish Gambusia affinis 2 0 0 902 226 367 150 99 0

Threespine Stickleback Gasterosteus aculeatus 3 0 3 9 25 4 0 0 121

Bay Pipefish Syngnathus leptorhynchus 0 0 0 0 0 0 0 0 287

Brown Rockfish Sebastes auriculatus 0 0 0 0 0 0 0 0 4

Lingcod Ophiodon elongatus 0 0 0 0 0 0 0 0 3
98

Table A.4. Continued.

Fish species

Trawl site Beach seine region

Sacramento Mossdale Chipps 

Island 1 2 3 4 5 6

Prickly Sculpin Cottus asper 0 4 0 9 33 34 17 5 1

Pacific Staghorn Sculpin Leptocottus armatus 0 0 7 0 2 17 0 0 335

Tidepool Sculpin Oligocottus maculosus 0 0 0 0 0 0 0 0 22

Cabezon Scorpaenichthys marmoratus 0 0 0 0 0 0 0 0 11

Striped Bass Morone saxatilis 3 1,594 1,061 6 126 65 61 46 26

Green Sunfish Lepomis cyanellus 4 2 0 5 2 0 0 0 0

Warmouth Lepomis gulosus 4 0 2 0 0 2 0 0 0

Bluegill Lepomis macrochirus 11 595 9 101 67 296 253 357 0

Redear Sunfish Lepomis microlophus 1 42 0 31 164 1,604 584 51 0

Smallmouth Bass Micropterus dolomieu 0 3 0 0 28 2 0 1 0

Spotted Bass Micropterus punctulatus 1 9 0 40 146 9 7 19 0

Largemouth Bass Micropterus salmoides 7 14 3 359 107 535 272 80 0

White Crappie Pomoxis annularis 0 4 1 7 3 10 0 0 0

Black Crappie Pomoxis nigromaculatus 2 13 0 81 2 8 3 17 0

Bigscale Logperch Percina macrolepida 0 8 0 497 110 104 27 18 0

White Croaker Genyonemus lineatus 0 0 0 0 0 0 0 0 1

Barred Surfperch Amphistichus argenteus 0 0 0 0 0 0 0 0 74

Shiner Perch Cymatogaster aggregata 0 0 0 0 0 0 0 0 246

Black Perch Embiotoca jacksoni 0 0 0 0 0 0 0 0 9

Walleye Surfperch Hyperprosopon argenteum 0 0 0 0 0 0 0 0 10

Tule Perch Hysterocarpus traskii 2 16 10 37 455 372 28 6 0

Dwarf Surfperch Micrometrus minimus 0 0 0 0 0 0 0 0 669

White Seaperch Phanerodon furcatus 0 0 0 0 0 0 0 0 18

Penpoint Gunnel Apodichthys flavidus 0 0 0 0 0 0 0 0 12

Saddleback Gunnel Pholis ornata 0 0 0 0 0 0 0 0 14
99

Table A.4. Continued.

Fish species

Trawl site Beach seine region

Sacramento Mossdale Chipps 

Island 1 2 3 4 5 6

Crevice Kelpfish Gibbonsia montereyensis 0 0 0 0 0 0 0 0 9

Yellowfin Goby Acanthogobius flavimanus 0 1 9 0 238 243 11 0 53

Arrow Goby Clevelandia ios 0 0 0 0 0 0 0 0 72

Bay Goby Lepidogobius lepidus 0 0 0 0 0 0 0 0 2

Shokihaze Goby Tridentiger barbatus 0 0 7 0 0 0 0 0 0

Shimofuri Goby Tridentiger bifasciatus 0 2 20 0 199 18 9 0 2

Chameleon Goby Tridentiger trigonocephalus 0 0 0 0 0 0 0 0 1

Rock Sole Lepidopsetta bilineata 0 0 0 0 0 0 0 0 1

California Halibut Paralichthys californicus 0 0 0 0 0 0 0 0 3

English Sole Parophrys vetulus 0 0 0 0 0 0 0 0 99

Starry Flounder Platichthys stellatus 0 0 20 0 0 0 0 0 7

Diamond Turbot Pleuronichthys guttulatus 0 0 0 0 0 0 0 0 9

Sand Sole Psettichthys melanostictus 0 0 0 0 0 0 0 0 7

Unidentified fish 0 1 0 0 0 0 0 0 0
100

Table A.5. Number of sample days and average number, standard deviation, and range of trawls 

per sample day for trawl sites within sample weeks during the 2012 field season.

Chipps Island (SB018M, N, S) Mossdale (SJ054M) Sacramento (SR055M)

Sample week 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

8/1/2011 3 9 (1.73) 7–10 3 10 (0) 10 3 10 (0) 10

8/7/2011 3 10 (0) 10 3 10 (0) 10 3 10 (0) 10

8/14/2011 3 10 (0) 10 3 10 (0) 10 3 10 (0) 10

8/21/2011 3 10 (0) 10 3 10 (0) 10 3 10 (0) 10

8/28/2011 3 8.7 (2.31) 6–10 3 9.3 (1.15) 8–10 3 8.7 (2.31) 6–10

9/4/2011 3 9.3 (1.15) 8–10 3 10 (0) 10 3 10 (0) 10

9/11/2011 3 10 (0) 10 3 10 (0) 10 3 10 (0) 10

9/18/2011 3 10 (0) 10 3 10 (0) 10 3 10 (0) 10

9/25/2011 3 10 (0) 10 3 10 (0) 10 3 10 (0) 10

10/2/2011 2 9.5 (0.71) 9–10 3 10 (0) 10 3 9.7 (0.58) 9–10

10/9/2011 3 10 (0) 10 3 10 (0) 10 3 10 (0) 10

10/16/2011 2 10 (0) 10 3 10 (0) 10 2 10 (0) 10

10/23/2011 1 10 (0) 10 3 10 (0) 10 3 10 (0) 10

10/30/2011 1 5 (0) 5 3 10 (0) 10 3 10 (0) 10

11/6/2011 1 1 (0) 1 3 10 (0) 10 3 10 (0) 10

11/13/2011 1 10 (0) 10 3 10 (0) 10 3 10 (0) 10

11/20/2011 1 6 (0) 6 3 9.3 (1.15) 8–10 3 8 (2.65) 5–10

11/27/2011 1 8 (0) 8 3 10 (0) 10 3 9.3 (1.15) 8–10

12/4/2011 3 9.7 (0.58) 9–10 3 10 (0) 10 3 10 (0) 10

12/11/2011 3 6 (4.58) 1–10 3 10 (0) 10 3 10 (0) 10

12/18/2011 2 5.5 (0.71) 5–6 3 8.7 (2.31) 6–10 3 7 (3.00) 4–10

12/25/2011 3 4 (1.00) 3– 5 3 9.3 (1.15) 8–10 3 9 (1.73) 7–10

1/1/2012 3 10 (0) 10 3 10 (0) 10 3 10 (0) 10

1/8/2012 2 8 (2.83) 6–10 3 10 (0) 10 3 10 (0) 10

1/15/2012 2 2.5 (0.71) 2–3 3 10 (0) 10 3 10 (0) 10

1/22/2012 2 6.5 (4.95) 3–10 3 10 (0) 10 3 10 (0) 10

1/29/2012 2 5 (2.83) 3–7 3 10 (0) 10 3 10 (0) 10

2/5/2012 2 9.5 (0.71) 9–10 3 9 (1.73) 7–10 3 10 (0) 10

2/12/2012 2 4 (1.41) 3–5 3 9.3 (1.15) 8–10 3 9 (1.73) 7–10

2/19/2012 2 9.5 (0.71) 9–10 3 10 (0) 10 3 10.3 (0.58) 10–11

2/26/2012 2 4 (0) 4 3 10 (0) 10 3 10 (0) 10

3/4/2012 2 9 (1.41) 8–10 3 10 (0) 10 3 10 (0) 10

3/11/2012 2 6.5 (4.95) 3–10 3 10 (0) 10 3 8.3 (2.89) 5–10

3/18/2012 2 10 (0) 10 3 10 (0) 10 3 10 (0) 10

3/25/2012 2 10 (0) 10 3 10 (0) 10 3 10 (0) 10
101

Table A.5. Continued.

Chipps Island (SB018M, N, S) Mossdale (SJ054M) Sacramento (SR055M)

Sample week 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

4/1/2012 2 7.5 (3.54) 5–10 5 10 (0) 10 3 10 (0) 10

4/8/2012 2 10 (0) 10 5 10 (0) 10 3 10 (0) 10

4/15/2012 2 10 (0) 10 5 10 (0) 10 3 10 (0) 10

4/22/2012 2 9.5 (0.71) 9–10 5 11 (2.24) 10–15 3 10 (0) 10

4/29/2012 2 8 (2.83) 6–10 5 10 (0) 10 2 10 (0) 10

5/6/2012 2 10 (0) 10 5 10.4 (0.89) 10–12 2 10 (0) 10

5/13/2012 2 10 (0) 10 5 10 (0) 10 2 10 (0) 10

5/20/2012 2 10 (0) 10 5 10 (0) 10 2 10 (0) 10

5/27/2012 2 10 (0) 10 5 10 (0) 10 2 10 (0) 10

6/3/2012 2 10 (0) 10 5 10 (0) 10 2 10 (0) 10

6/10/2012 2 7.5 (3.54) 5–10 4 10 (0) 10 2 10 (0) 10

6/17/2012 2 8.5 (0.71) 8–9 3 10 (0) 10 2 10 (0) 10

6/24/2012 2 7.5 (3.54) 5–10 3 10 (0) 10 2 10 (0) 10

7/1/2012 2 7.5 (0.71) 7–8 3 10 (0) 10 3 10 (0) 10

7/8/2012 2 7.5 (3.54) 5–10 3 10 (0) 10 3 10 (0) 10

7/15/2012 2 7.5 (3.54) 5–10 3 10 (0) 10 3 10 (0) 10

7/22/2012 2 9 (1.41) 8–10 3 10 (0) 10 3 10 (0) 10

7/29/2012 1 6 (0) 6 1 6 (0) 6 1 10 (0) 10
102

Table A.6. Number of sample days and average number, standard deviation, and range of trawls 

per sample day for trawl sites within sample weeks during the 2013 field season.

Chipps Island (SB018M ,N, S) Mossdale (SJ054M) Sacramento (SR055M)

Sample week 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

8/1/2012 1 10 (0) 10 2 10 (0) 10 2 10 (0) 10

8/5/2012 2 10 (0) 10 3 10 (0) 10 3 10 (0) 10

8/12/2012 2 7 (4.24) 4–10 3 10 (0) 10 3 10 (0) 10

8/19/2012 2 10 (0) 10 3 10 (0) 10 3 10 (0) 10

8/26/2012 2 7.5 (3.54) 5–10 3 10 (0) 10 3 10 (0) 10

9/2/2012 2 10 (0) 10 3 10 (0) 10 3 10 (0) 10

9/9/2012 2 10 (0) 10 3 10 (0) 10 3 10 (0) 10

9/16/2012 2 10 (0) 10 3 10 (0) 10 3 10 (0) 10

9/23/2012 2 9 (1.41) 8–10 3 10 (0) 10 3 10 (0) 10

9/30/2012 2 10 (0) 10 3 10 (0) 10 3 10 (0) 10

10/7/2012 2 6.5 (0.71) 6–7 3 10 (0) 10 3 10 (0) 10

10/14/2012 2 10 (0) 10 3 10 (0) 10 3 10 (0) 10

10/21/2012 3 8 (2.00) 6–10 3 8.3 (2.89) 5–10 3 10 (0) 10

10/28/2012 3 10 (0) 10 3 10 (0) 10 3 10 (0) 10

11/4/2012 3 10 (0) 10 3 10 (0) 10 3 10 (0) 10

11/11/2012 3 10 (0) 10 3 10 (0) 10 3 10 (0) 10

11/18/2012 3 10 (0) 10 3 9.7 (0.58) 9–10 3 10 (0) 10

11/25/2012 3 10 (0) 10 2 10 (0) 10 1 10 (0) 10

12/2/2012 3 2.7 (1.15) 2–4 3 9.3 (1.15) 8–10 3 7 (3.61) 3–10

12/9/2012 2 7 (2.83) 5–9 3 10 (0) 10 3 10 (0) 10

12/16/2012 3 10 (0) 10 3 10 (0) 10 3 10 (0) 10

12/23/2012 2 10 (0) 10 2 10 (0) 10 3 10.3 (8.08) 3–19

12/30/2012 3 10 (0) 10 3 10 (0) 10 3 10.3 (0.58) 10–11

1/6/2013 3 10 (0) 10 3 10 (0) 10 3 10 (0) 10

1/13/2013 3 10 (0) 10 3 10 (0) 10 3 10 (0) 10

1/20/2013 3 10 (0) 10 3 10 (0) 10 3 10 (0) 10

1/27/2013 3 10 (0) 10 3 10 (0) 10 3 10 (0) 10

2/3/2013 3 10 (0) 10 3 10 (0) 10 3 10 (0) 10

2/10/2013 3 9.3 (1.15) 8–10 3 10 (0) 10 3 10 (0) 10

2/17/2013 3 10 (0) 10 3 10 (0) 10 3 10 (0) 10

2/24/2013 3 10 (0) 10 3 10 (0) 10 3 10 (0) 10

3/3/2013 3 10 (0) 10 3 10 (0) 10 3 10 (0) 10

3/10/2013 3 10 (0) 10 3 10 (0) 10 3 10 (0) 10

3/17/2013 3 10 (0) 10 3 10 (0) 10 3 10 (0) 10

3/24/2013 3 10 (0) 10 3 10 (0) 10 3 10 (0) 10

3/31/2013 3 10 (0) 10 4 10 (0) 10 3 10 (0) 10

4/7/2013 3 10 (0) 10 5 10 (0) 10 3 10 (0) 10
103

Table A.6. Continued.

Chipps Island (SB018M, N, S) Mossdale (SJ054M) Sacramento (SR055M)

Sample week 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

4/14/2013 3 10 (0) 10 4 12.25 (4.50) 10–19 3 10 (0) 10

4/21/2013 3 10 (0) 10 5 11 (2.24) 10–15 3 10 (0) 10

4/28/2013 3 10 (0) 10 5 10.4 (0.89) 10–12 2 10 (0) 10

5/5/2013 3 10 (0) 10 5 10.2 (0.45) 10–11 2 10 (0) 10

5/12/2013 3 10 (0) 10 5 11 (2.24) 10–15 2 10 (0) 10

5/19/2013 3 10 (0) 10 5 10 (0) 10 2 10 (0) 10

5/26/2013 3 10 (0) 10 4 10 (0) 10 2 10 (0) 10

6/2/2013 3 10 (0) 10 5 10 (0) 10 2 10 (0) 10

6/9/2013 3 10 (0) 10 3 10 (0) 10 2 10 (0) 10

6/16/2013 3 10 (0) 10 3 10 (0) 10 2 10 (0) 10

6/23/2013 3 10 (0) 10 3 10 (0) 10 2 10 (0) 10

6/30/2013 3 9.3 (1.15) 8–10 3 10 (0) 10 3 10 (0) 10

7/7/2013 3 10 (0) 10 3 10 (0) 10 3 10 (0) 10

7/14/2013 3 10 (0) 10 3 10 (0) 10 3 10 (0) 10

7/21/2013 3 10 (0) 10 3 10 (0) 10 3 10 (0) 10

7/28/2013 2 10 (0) 10 2 10 (0) 10 2 10 (0) 10
104

Table A.7. Beach seine sites that fish samples were collected at least once within a sample 

week in the Lower Sacramento River Seine Region during the 2012 field season.

Sample Station code

week SR144W SR138E SR130E SR094E SR119E SR090W SR080E SR071E

8/1//2011 X X X X X X X

8/7/2011 X X X X X X X

8/14/2011 X X X X X X

8/21/2011 X X X X X

8/28/2011 X X X X X X X

9/4/2011 X X X X X X X

9/11/2011 X X X X X X X

9/18/2011 X X X X X X

9/25/2011 X X X X

10/2/2011 X X X X X X

10/9/2011 X X X X X X X

10/16/2011 X X X X X X X

10/23/2011 X X X X X X

10/30/2011 X X X X X X X

11/6/2011 X X X X X X

11/13/2011 X X X X X X

11/20/2011 X X X X X X X

11/27/2011 X X X X X X X

12/4/2011 X X X X X X

12/11/2011 X X X X X

12/18/2011 X X X X X X

12/25/2011 X X X X X X

1/1/2012 X X X X

1/8/2012 X X X X X

1/15/2012 X X X X X

1/22/2012 X X X X X

1/29/2012 X X X X X X X

2/5/2012 X X X X

2/12/2012 X X X X X X X

2/19/2012 X X X X X X

2/26/2012 X X X X X X

3/4/2012 X X X X X X

3/11/2012 X X X X X X

3/18/2012 X X X X X X X

3/25/2012 X X X X X

4/1/2012 X X X X X X

4/8/2012 X X X X X X X X

4/15/2012 X X X X

4/22/2012 X X X X X X X X
105

Table A.7. Continued.

Sample Station code

week SR144W SR138E SR130E SR094E SR119E SR090W SR080E SR071E

4/29/2012 X X X X X

5/6/2012 X X X X

5/13/2012 X X X X X X

5/20/2012 X X X X X X X

5/27/2012 X X X X X

6/3/2012 X X X X X

6/10/2012 X X X X X X

6/17/2012 X X X X X X

6/24/2012 X X X X X X

7/1/2012 X X X X X X

7/8/2012 X X X X X

7/15/2012 X X X X X X

7/22/2012 X X X X X X X

7/29/2012 X X X X X X
106

Table A.8. Beach seine sites that fish samples were collected at least once within a sample week 

in the Lower Sacramento River Seine Region during the 2013 field season.

Sample Station code

week SR144W SR138E SR130E SR119E SR094E SR090W SR080E SR071E

8/1/2012

8/5/2012 X X X X X X

8/12/2012 X X X X X X

8/19/2012 X X X X X X

8/26/2012 X X X X X X

9/2/2012 X X X X X

9/9/2012 X X X X

9/16/2012 X X X X X X X

9/23/2012 X X X X X X

9/30/2012 X X X X X

10/7/2012 X X X X X X

10/14/2012 X X X X X X

10/21/2012 X X X X X X X

10/28/2012 X X X X X X X

11/4/2012 X X X X X X

11/11/2012 X X X X X

11/18/2012 X X X X X X X

11/25/2012 X X X X X X

12/2/2012 X X X X X

12/9/2012 X X X X X X

12/16/2012 X X X X X X

12/23/2012 X X X X X X

12/30/2012 X X X X X X X

1/6/2013 X X X X X

1/13/2013 X X X X X X

1/20/2013 X X X X X X

1/27/2013 X X X X X X X

2/3/2013 X X X X X X X

2/10/2013 X X X X X X X

2/17/2013 X X X X X X X

2/24/2013 X X X X X

3/3/2013 X X X X X X

3/10/2013 X X X X X

3/17/2013 X X X X X X

3/24/2013 X X X X X X

3/31/2013 X X X X X X X

4/7/2013 X X X X X X X

4/14/2013 X X X X X X X

4/21/2013 X X X X X
107

Table A.8. Continued.

Sample Station code

week SR144W SR138E SR130E SR119E SR094E SR090W SR080E SR071E

4/28/2013 X X X X X X

5/5/2013 X X X X X X

5/12/2013 X X X X X X X

5/19/2013 X X X X X X X

5/26/2013 X X X X X X X X

6/2/2013 X X X X X X X

6/9/2013 X X X X X X

6/16/2013 X X X X X X

6/23/2013 X X X X X X X

6/30/2013 X X X X X X

7/7/2013 X X X X X X X

7/14/2013 X X X X X X

7/21/2013 X X X X X X X

7/28/2013
108

Table A.9. Beach seine sites that fish samples were collected at least once within a sample week 

in the North Delta Seine Region during the 2012 field season.

Sample Station code

week SR060E AM001S SR049E SR043W SS011N XC001N SF014E GS010E SR024E SR017E

8/1/2011 X X X X X X X X

8/7/2011 X X X X X X X X X

8/14/2011 X X X X X X X X X

8/21/2011 X X X X X X X X

8/28/2011 X X X X X X X X

9/4/2011 X X X X X X X X X

9/11/2011 X X X X X X

9/18/2011 X X X X X X X X X

9/25/2011 X X X X X X X X X

10/2/2011 X X X X X X X X X

10/9/2011 X X X X X X X X

10/16/2011 X X X X X X X X

10/23/2011 X X X X X X X

10/30/2011 X X X X X X X X

11/6/2011 X X X X X X X

11/13/2011 X X X X X X X X X

11/20/2011 X X X X X X X X X

11/27/2011 X X X X X X X X X X

12/4/2011 X X X X X X X X X

12/11/2011 X X X X X X X X X

12/18/2011 X X X X X X X X

12/25/2011 X X X X X X X X X X

1/1/2012 X X X X X X X X X X

1/8/2012 X X X X X X X X X

1/15/2012 X X X X X X X X X

1/22/2012 X X X X X X X X

1/29/2012 X X X X X X X X

2/5/2012 X X X X X X X X X X

2/12/2012 X X X X X X X X X

2/19/2012 X X X X X X X X X

2/26/2012 X X X X X X X X

3/4/2012 X X X X X X X X

3/11/2012 X X X X X X X X

3/18/2012 X X X X X X X X X

3/25/2012 X X X X X X X X X

4/1/2012 X X X X

4/8/2012 X X X X X X X X X

4/15/2012 X X X X X X X X X

4/22/2012 X X X X X X X X X
109

Table A.9. Continued.

Sample Station code

week SR060E AM001S SR049E SR043W SS011N XC001N SF014E GS010E SR024E SR017E

4/29/2012 X X X X X X X X X

5/6/2012 X X X X X X X X X

5/13/2012 X X X X X X X X X

5/20/2012 X X X X X X X X X

5/27/2012 X X X X X X X X

6/3/2012 X X X X X X X X X

6/10/2012 X X X X X X X X X X

6/17/2012 X X X X X X X

6/24/2012 X X X X X X X X

7/1/2012 X X X X X X X X

7/8/2012 X X X X X X X X X X

7/15/2012 X X X X X X X X

7/22/2012 X X X X X X X X

7/29/2012 X X X X X X X X
110

Table A.10. Beach seine sites that fish samples were collected at least once within a sample week 

in the North Delta Seine Region during the 2013 field season.

Sample Station code

week SR060E AM001S SR049E SR043W SS011N XC001N SF014E GS010E SR024E SR017E SR015E

8/1/2012

8/5/2012

8/12/2012 X X X X X X X X

8/19/2012 X X X X X X X

8/26/2012 X X X X X X X X

9/2/2012 X X X X X X X X X

9/9/2012 X X X X X X X X X

9/16/2012 X X X X X X X X

9/23/2012 X X X X X X X X X X

9/30/2012 X X X X X X X

10/7/2012 X X X X X X X X

10/14/2012 X X X X X X X X X

10/21/2012 X X X X X X X X X X

10/28/2012 X X X X X X X X X X

11/4/2012 X X X X X X X X X X X

11/11/2012 X X X X X X X X X X

11/18/2012 X X X X X X X X X X

11/25/2012 X X X X X X X X X

12/2/2012 X X X X X X X

12/9/2012 X X X X X X X

12/16/2012 X X X X X X X X

12/23/2012 X X X X X X

12/30/2012 X X X X X X X

1/6/2013 X X X X X X X X X X

1/13/2013 X X X X X X X X X

1/20/2013 X X X X X X X X X

1/27/2013 X X X X X X X X

2/3/2013 X X X X X X X X

2/10/2013 X X X X X X

2/17/2013 X X X X X X X

2/24/2013 X X X X X X

3/3/2013 X X X X X X X X X

3/10/2013 X X X X X X X X X

3/17/2013 X X X X X X X X X

3/24/2013 X X X X X X X X X

3/31/2013 X X X X X X X X

4/7/2013 X X X X X X X X

4/14/2013 X X X X X X X X X X

4/21/2013 X X X X X X X X X
111

Table A.10. Continued.

Sample Station code

week SR060E AM001S SR049E SR043W SS011N XC001N SF014E GS010E SR024E SR017E SR015E

4/28/2013 X X X X X X X X

5/5/2013 X X X X X X X

5/12/2013 X X X X X X X

5/19/2013 X X X X X X X X X

5/26/2013 X X X X X X X X X

6/2/2013 X X X X X

6/9/2013 X X X X X X X

6/16/2013 X X X X X X X X

6/23/2013 X X X X X X

6/30/2013 X X X X X X

7/7/2013 X X X X X X X X X

7/14/2013 X X X X X X X X X

7/21/2013 X X X X X X X

7/28/2013 X X X X X X X X X X
112

Table A.11. Beach seine sites that fish samples were collected at least once within a sample week 

in the Central Delta Seine Region during the 2012 field season.

Sample Station code

week DS002S LP003E MK004W SR014W SR012W TM001N MS001N SJ005N SJ001S

8/1/2011 X X X X X X X X

8/7/2011 X X X X X X X X X

8/14/2011 X X X X X X X X X

8/21/2011 X X X X X X

8/28/2011 X X X X X X X X X

9/4/2011 X X X X X X X X X

9/11/2011 X X X X X X X X

9/18/2011 X X X X X X X X

9/25/2011 X X X X X X X

10/2/2011 X X X X X X X X X

10/9/2011 X X X X X X X X

10/16/2011 X X X X X X X

10/23/2011 X X X X X X X X X

10/30/2011 X X X X X X X X

11/6/2011 X X X X X X X X

11/13/2011 X X X X X X X X X

11/20/2011 X X X

11/27/2011 X X X X

12/4/2011 X X X X X X X

12/11/2011 X X X X X X X

12/18/2011 X X X X

12/25/2011 X X X X X X X

1/1/2012 X X X X X X

1/8/2012 X X X X X X X X

1/15/2012 X X X X X X X X X

1/22/2012 X X X X X X X X

1/29/2012 X X X X X X X X

2/5/2012 X X X X X X X X X

2/12/2012 X X X X X X X

2/19/2012 X X X X X X X X

2/26/2012 X X X X X X X X

3/4/2012 X X X X X X X

3/11/2012 X X X X X X

3/18/2012 X X X X X X

3/25/2012 X X X X X X X X X

4/1/2012 X X X X X X X X X

4/8/2012 X X X X X X

4/15/2012 X X X X X X X X X

4/22/2012 X X X X X X X X X
113

Table A.11. Continued.

Sample Station code

week DS002S LP003E MK004W SR014W SR012W TM001N MS001N SJ005N SJ001S

4/29/2012 X X X X X X X X X

5/6/2012 X X X X X X X X

5/13/2012 X X X X X X X X X

5/20/2012 X X X X X X X X X

5/27/2012 X X X X X X X X X

6/3/2012 X X X X X

6/10/2012 X X X X X X X

6/17/2012 X X X X X X X X X

6/24/2012 X X X X X X X

7/1/2012 X X X X X X X X

7/8/2012 X X X X X X X X X

7/15/2012 X X X X X X X

7/22/2012 X X X X X X X X X

7/29/2012
114

Table A.12. Beach seine sites that fish samples were collected at least once within a sample week 

in the Central Delta Seine Region during the 2013 field season.

Sample Station code

week DS002S LP003E MK004W SR014W SR012W TM001N MS001N SJ005N SJ001S

8/1/2012 X X X X X X X

8/5/2012 X X X X X X X X X

8/12/2012 X X X X X X X

8/19/2012 X X X X X X X X X

8/26/2012 X X X X X X X X X

9/2/2012 X X X X X X X

9/9/2012 X X X X X X X

9/16/2012 X X X X X X X

9/23/2012 X X X X X X X X X

9/30/2012 X X X X X X

10/7/2012 X X X X X X

10/14/2012 X X X X X X

10/21/2012 X X X X X X X X

10/28/2012 X X X X X X X X X

11/4/2012 X X X X X

11/11/2012 X X X X X X X X

11/18/2012 X X X X

11/25/2012 X X X X X X X X

12/2/2012 X X X X X X

12/9/2012 X X X X X

12/16/2012 X X X X X X X X

12/23/2012 X X X X X X

12/30/2012 X X X X X X X

1/6/2013 X X X X X X

1/13/2013 X X X X X X X X X

1/20/2013 X X X X X X X

1/27/2013 X X X X X X X

2/3/2013 X X X X X X X

2/10/2013 X X X X X X X X X

2/17/2013 X X X X X X X X

2/24/2013 X X X X X X X X

3/3/2013 X X X X X X X

3/10/2013 X X X X X X X X

3/17/2013 X X X X X X

3/24/2013 X X X X X X X X

3/31/2013 X X X X X X X X

4/7/2013 X X X X X X X X X

4/14/2013 X X X X X X X

4/21/2013 X X X X X X X X
115

Table A.12. Continued.

Sample Station code

week DS002S LP003E MK004W SR014W SR012W TM001N MS001N SJ005N SJ001S

4/28/2013 X X X X X X X X

5/5/2013 X X X X X X X X

5/12/2013 X X X X X X X X X

5/19/2013 X X X X X X X X

5/26/2013 X X X X X X X X

6/2/2013 X X X X X X X X X

6/9/2013 X X X X X X X X X

6/16/2013 X X X X X X X

6/23/2013 X X X X X X X X

6/30/2013 X X X X X X X X

7/7/2013 X X X X X X X

7/14/2013 X X X X X X X

7/21/2013 X X X X X X X

7/28/2013 X X X X X X X
116

Table A.13. Beach seine sites that fish samples were collected at least once within a sample week in 

the South Delta Seine Region during the 2012 field season.

Sample Station code

week SJ041N SJ032S SJ026S OR003W WD002W OR014W OR019E OR023E MR010W SJ051E

8/1/2011 X

8/7/2011 X X X X X X X

8/14/2011

8/21/2011 X X X X X

8/28/2011 X X X X X X X

9/4/2011 X X X X X X

9/11/2011 X X X X X

9/18/2011 X X X X

9/25/2011 X X X X X X

10/2/2011 X X X

10/9/2011 X X X X X X

10/16/2011 X X X X

10/23/2011 X X X X X X X

10/30/2011 X X

11/6/2011 X X X X X X

11/13/2011 X X X

11/20/2011 X X X

11/27/2011 X X X

12/4/2011 X X

12/11/2011 X X

12/18/2011 X X

12/25/2011 X X X X X X

1/1/2012 X X X X

1/8/2012 X X X X X X X

1/15/2012 X X

1/22/2012 X X X X X X X

1/29/2012 X X

2/5/2012 X X X X X

2/12/2012 X X X X

2/19/2012 X X X X X X X X

2/26/2012 X X

3/4/2012 X X X X X X X X X X

3/11/2012 X X X

3/18/2012 X X X X X X X X

3/25/2012 X X X

4/1/2012 X X X X X X X X

4/8/2012 X X

4/15/2012 X X X X X X X

4/22/2012 X
117

Table A.13. Continued.

Sample Station code

week SJ041N SJ032S SJ026S OR003W WD002W OR014W OR019E OR023E MR010W SJ051E

4/29/2012 X X X X X X X

5/6/2012 X

5/13/2012 X X X X X X X X

5/20/2012 X

5/27/2012 X X X X X X X X X X

6/3/2012 X X

6/10/2012 X X X X X X X X

6/17/2012 X X X

6/24/2012 X X X X X X X X

7/1/2012 X X X X

7/8/2012 X X X

7/15/2012 X X X X X

7/22/2012 X X X X X

7/29/2012 X X X X X X X X
118

Table A.14. Beach seine sites that fish samples were collected at least once within a sample week in 

the South Delta Seine Region during the 2013 field season.

Sample Station code

week SJ041N SJ032S SJ026S OR003W WD002W OR014W OR019E OR023E MR010W SJ051E

8/1/2012

8/5/2012 X X X

8/12/2012 X X X X X X

8/19/2012

8/26/2012 X X X X X X X

9/2/2012 X X X

9/9/2012 X X X X X X

9/16/2012 X X

9/23/2012 X X X X X

9/30/2012 X

10/7/2012 X X X

10/14/2012 X X X

10/21/2012 X X X X X X X

10/28/2012 X X X X X X X

11/4/2012

11/11/2012 X X X X

11/18/2012 X X X X X X

11/25/2012 X X X X

12/2/2012 X

12/9/2012 X X X X X X

12/16/2012 X

12/23/2012 X

12/30/2012 X X X

1/6/2013 X X X X X X X X

1/13/2013 X X X

1/20/2013 X X X X X X X X

1/27/2013 X X X X X X X X

2/3/2013 X X X

2/10/2013 X X X X X X

2/17/2013 X X X X X X

2/24/2013 X X X X X X X X X

3/3/2013 X X X X X

3/10/2013 X X X X X X X X X X

3/17/2013 X X X X X X X X

3/24/2013 X X X X X X X X X

3/31/2013 X X X

4/7/2013 X X X X X X X X X

4/14/2013 X X

4/21/2013 X X X X X X X X
119

Table A.14. Continued.

Sample Station code

week SJ041N SJ032S SJ026S OR003W WD002W OR014W OR019E OR023E MR010W SJ051E

4/28/2013 X X X X

5/5/2013 X X X X X X X X X X

5/12/2013 X X X X X

5/19/2013 X X X X X X X X X

5/26/2013 X X

6/2/2013 X X X X X X X X

6/9/2013 X X

6/16/2013 X X X X X X X X X

6/23/2013 X X

6/30/2013 X X X X X X X X

7/7/2013 X X X X X X

7/14/2013 X X X X X X X X

7/21/2013 X X X X

7/28/2013
120

Table A.15. Beach seine sites that fish samples were collected at least once within a sample week in the Lower 

San Joaquin River Seine Region during the 2012 field season.

Sample Station code

week SJ083W SJ079E SJ077E SJ076W SJ074W SJ074A SJ070N SJ068W SJ065W SJ063W SJ058W SJ056E

8/1/2011 X X X X X X

8/7/2011 X X X X X

8/14/2011

8/21/2011

8/28/2011 X X X X X X

9/4/2011

9/11/2011 X X X X X X

9/18/2011

9/25/2011 X X X X X X

10/2/2011

10/9/2011 X X X X X X

10/16/2011

10/23/2011 X X X X X X

10/30/2011

11/6/2011 X X X X X

11/13/2011

11/20/2011 X X X X X

11/27/2011

12/4/2011 X X X

12/11/2011

12/18/2011 X X X

12/25/2011

1/1/2012 X X X X X

1/8/2012 X X X X X

1/15/2012 X X X

1/22/2012 X X

1/29/2012 X X X

2/5/2012 X X X X X X X

2/12/2012 X X X X X X

2/19/2012 X X X X X X

2/26/2012 X X X X X X

3/4/2012 X X X X X X X

3/11/2012 X X X X X X X

3/18/2012 X X X X X X

3/25/2012 X X X X X X

4/1/2012 X X X X X

4/8/2012 X X X X X

4/15/2012

4/22/2012 X X X X X X
121

Table A.15. Continued.

Sample Station code

week SJ083W SJ079E SJ077E SJ076W SJ074W SJ074A SJ070N SJ068W SJ065W SJ063W SJ058W SJ056E

4/29/2012 X X X X X

5/6/2012 X X X

5/13/2012 X X X X

5/20/2012 X X X X X

5/27/2012 X X X X X

6/3/2012 X X X X X X

6/10/2012 X X X X X X X

6/17/2012 X X X X X X X

6/24/2012 X X X X X X X

7/1/2012 X X X X X X

7/8/2012

7/15/2012 X X X X X

7/22/2012

7/29/2012 X X X X
122

Table A.16. Beach seine sites that fish samples were collected at least once within a 

sample week in the Lower San Joaquin River Region during the 2013 field season.

Sample Station code

week SJ083W SJ077E SJ074W SJ068W SJ063W SJ058W SJ056E

8/1/2012

8/5/2012

8/12/2012 X X X X X

8/19/2012

8/26/2012 X X X X X X

9/2/2012

9/9/2012 X X X X X

9/16/2012

9/23/2012 X X X X X X X

9/30/2012 X X X X X X X

10/7/2012

10/14/2012 X X X X X

10/21/2012

10/28/2012 X X X X X X X

11/4/2012

11/11/2012 X X X X X X X

11/18/2012

11/25/2012 X X X X X

12/2/2012

12/9/2012 X

12/16/2012

12/23/2012 X X X

12/30/2012 X X X X X

1/6/2013 X X X X X X X

1/13/2013 X X X X X X X

1/20/2013 X X X X X X X

1/27/2013 X X X X X X X

2/3/2013 X X X X X X

2/10/2013 X X X X X

2/17/2013 X X X X X X X

2/24/2013 X X X X X X

3/3/2013 X X X X X X

3/10/2013 X X X X X X X

3/17/2013 X X X X X X X

3/24/2013 X X X X X X

3/31/2013 X X X X X X

4/7/2013 X X X X X X

4/14/2013 X X X X X X X

4/21/2013 X X X X X
123

Table A.16. Continued.

Sample Station Code

week SJ083W SJ077E SJ074W SJ068W SJ063W SJ058W SJ056E

4/28/2013 X X X X X X

5/5/2013 X X X X X X

5/12/2013 X X X X X X X

5/19/2013 X X X X X X X

5/26/2013 X X X X X X X

6/2/2013 X X X X X X X

6/9/2013 X X X X X X X

6/16/2013 X X X X X X

6/23/2013 X X X X X

6/30/2013

7/7/2013 X X X X X X

7/14/2013

7/21/2013

7/28/2013
124

Table A.17. Beach seine sites that fish samples were collected at least once within a sample week 

in the San Francisco and San Pablo Bays Region during the 2012 field season.

Sample Station code

week SA010W SA004W SA008W SP000W SP001W SP003E SA009E SA007E SA001M

8/1/2011 X X

8/7/2011 X X X X

8/14/2011 X X X X

8/21/2011 X X X X

8/28/2011 X X X X

9/4/2011 X X X X

9/11/2011 X X X X X

9/18/2011 X X X X

9/25/2011 X X X X X

10/2/2011 X X X X

10/9/2011 X X X X X

10/16/2011 X X X X

10/23/2011 X X X X X

10/30/2011 X X X X

11/6/2011 X X X X X

11/13/2011 X X X X

11/20/2011 X X X X X

11/27/2011 X X X X

12/4/2011 X X X X X

12/11/2011 X X X X

12/18/2011 X X X X

12/25/2011 X X X X

1/1/2012 X X X X

1/8/2012 X X X X

1/15/2012 X X X X X

1/22/2012 X X X X

1/29/2012 X X X X

2/5/2012 X X X X

2/12/2012 X X X X

2/19/2012 X X X X

2/26/2012 X X X X

3/4/2012 X X X X

3/11/2012 X X X X

3/18/2012 X X X

3/25/2012 X X X

4/1/2012 X X X

4/8/2012 X X

4/15/2012 X X X

4/22/2012 X X X
125

Table A.17. Continued.

Sample Station code

week SA010W SA004W SA008W SP000W SP001W SP003E SA009E SA007E SA001M

4/29/2012 X X X X

5/6/2012 X X

5/13/2012 X X X X

5/20/2012 X X

5/27/2012 X X X X

6/3/2012 X X

6/10/2012 X X X X

6/17/2012 X X

6/24/2012 X X X X

7/1/2012 X X

7/8/2012 X X X X

7/15/2012 X X

7/22/2012 X X X X

7/29/2012
126

Table A.18. Beach seine sites that fish samples were collected at least once within a sample week 

in the San Francisco and San Pablo Bays Region during the 2013 field season.

Sample Station code

week SA010W SA004W SA008W SP000W SP001W SP003E SA009E SA007E SA001M

8/1/2012 X X

8/5/2012 X X X X

8/12/2012 X X X X X

8/19/2012 X X X

8/26/2012 X X X X

9/2/2012 X X X X

9/9/2012 X X X X

9/16/2012 X X X

9/23/2012 X X X X X

9/30/2012 X X X X

10/7/2012 X X X X X

10/14/2012 X X X X

10/21/2012 X X X X X

10/28/2012 X X X

11/4/2012 X X X X

11/11/2012 X X X X

11/18/2012 X X X X

11/25/2012 X X X X

12/2/2012 X X X X

12/9/2012 X X

12/16/2012 X X X X

12/23/2012 X X X X

12/30/2012 X X X X

1/6/2013 X X X X

1/13/2013 X X X X

1/20/2013 X X X X

1/27/2013 X X X X X

2/3/2013 X X X X

2/10/2013 X X

2/17/2013 X X X X

2/24/2013 X X X X X

3/3/2013 X X X X

3/10/2013 X X X X X

3/17/2013

3/24/2013 X X X X X X X X X

3/31/2013 X X X X

4/7/2013 X X

4/14/2013 X X X X

4/21/2013 X X X X X
127

Table A.18. Continued.

Sample Station code

week SA010W SA004W SA008W SP000W SP001W SP003E SA009E SA007E SA001M

4/28/2013 X X X X X

5/5/2013 X X X X

5/12/2013 X X X X

5/19/2013 X X X X

5/26/2013 X X

6/2/2013 X X X X

6/9/2013 X X

6/16/2013 X X X X X

6/23/2013 X X X

6/30/2013 X X X X

7/7/2013 X X

7/14/2013 X X X X

7/21/2013 X X X

7/28/2013
128

Table A.19. Water year types for the Sacramento and San Joaquin River basins 

from 1978 to 2013 (CDWR 2014b). 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

2012 BN D

2013 D C
129

Table A.20. Recoveries of all coded wire tagged juvenile winter-, fall-, late fall-, and spring-run 

Chinook Salmon by the DJFMP and fish facilities during the 2012 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 (MokeFH), Nimbus Fish Hatchery 

(NimbFH), and Merced River Fish Facility (MercFF; PSMFC 2014).

 Recovery location

Release location

(hatchery of origin)

Region 1Region 2Region 3Region 4Region 5Region 6

Sacramento 

Trawl Site

Mossdale

Trawl Site

Chipps Island 

Trawl Site

DJFMP total

Winter-run

 Caldwell Park (LivinNFH) 0 0 0 0 0 0 13 0 8 21

Fall-run

 American River (NimbFH) 0 1 0 0 0 0 57 0 60 118

 Battle Creek (ColemNFH) 0 1 0 0 0 0 211 0 112 324

 Elkhorn (FeathFH) 10 0 0 0 0 0 15 0 14 40

 Hatfield SP (MercFF) 0 0 0 0 1 0 0 121 0 122

 Mare Is. (NimbFH) 0 0 0 0 0 0 0 0 2 2

 Merced River (MercFH) 0 0 0 1 0 0 0 1027 2 1028

 Mokelumne River (MokeFH) 0 0 0 0 0 0 0 0 1 1

 San Pablo Bay (FeathFH) 0 0 0 0 0 1 0 0 4 5

 Sherman Island (MokeFH) 0 0 0 0 0 0 0 0 175 175

 Yolo Bypass (FeathFH) 0 0 0 0 0 0 0 0 0 1

Late fall-run

 Battle Creek (ColemNFH) 1 2 0 0 0 0 27 0 22 52

Spring-run

 Boyd’s Ramp (FeathFH) 2 12 2 0 0 0 90 0 112 218

 Thermalito BP (FeathFH) 0 0 0 0 0 0 1 0 5 6

 San Pablo Bay (FeathFH) 0 0 0 0 0 0 0 0 1 1

Unknown 0 0 0 0 0 0 11 49 15 75
130

Table A.21. Recoveries of all coded wire tagged juvenile winter-, fall-, late fall-, and springrun Chinook Salmon by the DJFMP during the 2013 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 (MokeFH), Nimbus Fish Hatchery 

(NimbFH), and Merced River Fish Facility (MercFF; PSMFC 2014).

 Recovery location

Release location

(hatchery of origin)

Region 1Region 2Region 3Region 4Region 5Region 6

Sacramento 

Trawl Site

Mossdale Trawl 

Site

Chipps Island 

Trawl Site

DJFMP total

Winter-run

 Caldwell Park (LivinNFH) 7 0 0 0 0 0 1 0 1 9

Fall-run

 American River (NimbFH) 0 0 0 0 0 0 99 0 74 173

 Battle Creek (ColemNFH) 4 0 1 0 0 0 204 0 134 343

 Elkhorn (FeathFH) 2 0 0 0 0 0 4 0 1 7

 Jersey Point (MercFF) 0 0 0 0 0 0 0 0 33 72

 Mokelumne River (MokeFH) 0 0 0 0 0 0 0 0 1 1

 Mossdale (MercFF) 0 0 0 0 0 0 0 39a0 39a

 Sherman Is. (MokeFH) 0 0 0 0 0 0 0 0 270 270

 San Pablo Bay (FeathFH) 0 0 0 0 0 0 0 0 4 4

 Yolo Bypass (FeathFH) 2 0 0 0 0 0 0 0 0 2

Late fall-run

 Battle Creek (ColemNFH) 12 26 0 0 0 0 34 0 68 140

Spring-run

 Boyd’s Ramp (FeathFH) 1 0 1 0 0 0 215 0 80 297

 Crockett (FeathFH) 0 0 0 0 0 0 0 0 18 18

 Gridley (FeathFH) 0 0 0 0 0 0 1 0 2 3

Unknown 3 1 0 0 0 0 10 6 14 34

a RMIS lists release location as Jersey Point, however notes that a proportion of fish were 

released at Mossdale due to truck malfunction (PSMFC 2014). These fish were assumed to 

have been released at Mossdale. 
131

Table A.22. Total adult Chinook Salmon escapement estimates by race 

for the Sacramento and San Joaquin River basins from 1978 to 2013 

(CDFW 2014).

Year Winter-run Fall-run Late fall-run Spring-run

1978 25,012 156,962 12,479 8,126

1979 2,364 227,646 10,284 3,116

1980 1,156 172,137 9,093 12,464

1981 22,797 260,259 6,718 22,105

1982 1,281 230,706 6,899 27,890

1983 1,831 205,290 15,089 7,958

1984 2,763 262,907 10,388 9,599

1985 5,407 356,304 10,180 15,221

1986 2,596 297,820 8,301 25,696

1987 2,185 301,583 16,571 13,888

1988 2,878 268,436 13,218 18,933

1989 696 182,350 12,872 12,163

1990 430 87,853 8,078 7,683

1991 211 132,455 8,263 5,926

1992 1,240 110,413 10,131 3,044

1993 387 165,423 1,267 6,076

1994 186 220,667 889 6,187

1995 1,297 330,168 489 15,238

1996 1,337 351,551 1,385 9,083

1997 880 402,797 4,578 5,193

1998 2,992 246,026 42,419 31,649

1999 3,288 414,259 15,758 10,100

2000 1,352 485,681 12,883 9,244

2001 8,224 624,631 21,813 26,663

2002 7,441 872,669 40,406 25,043

2003 8,218 590,992 8,882 30,697

2004 7,869 386,848 14,150 17,150

2005 15,839 437,693 16,282 23,093

2006 17,296 292,954 15,089 12,906

2007 2,541 97,168 18,843 11,144

2008 2,830 71,291 10,372 13,387

2009a4,537 53,129 10,318 4,505

2010 a1,596 163,190 9,986 4,623

2011 a827 227,889 8,446 7,408

2012 a2,674 341,823 5,969 22,249

2013 a6,123 453,650 8,953 23,697

a

indicates years containing preliminary data
132

Table A.23. 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 2012 field season.

Sample Station codes

week SR080E SR071E SR062E SR060E AM001S SR057E SR055E SR049E

10/2/2011 3 3 3 3 1 3 3 3

10/9/2011 3 3 3 3 1 3 3 2

10/16/2011 3 3 3 3 1 3 3 2

10/23/2011 3 3 2 3 1 2 3 2

10/30/2011 3 3 2 3 1 3 3 3

11/6/2011 3 3 3 3 1 3 3 3

11/13/2011 3 3 2 3 1 3 2 2

11/20/2011 3 3 3 3 1 3 3 3

11/27/2011 3 3 2 3 1 3 3 3

12/4/2011 3 3 3 3 1 3 3 3

12/11/2011 3 3 3 3 1 3 3 3

12/18/2011 3 3 3 3 1 3 3 2

12/25/2011 3 3 2 3 1 3 3 3

1/1/2012 1 1 1 1 1 1 1 1

1/8/2012 1 1 0 1 1 1 1 1

1/15/2012 1 1 1 1 1 1 1 1

1/22/2012 1 1 1 1 0 1 1 1

1/29/2012 2 2 0 2 1 1 1 2
133

Table A.24. 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 2013 field season.

Sample Station code

week SR080E SR071E SR062E SR060E AM001S SR057E SR055E SR049E

9/30/2012 3 3 3 3 1 3 3 1

10/7/2012 3 3 3 3 1 2 3 3

10/14/2012 3 3 2 3 1 3 3 3

10/21/2012 3 3 3 3 1 3 3 3

10/28/2012 3 3 3 3 1 3 3 3

11/4/2012 3 3 3 3 1 3 3 3

11/11/2012 3 3 3 3 1 3 3 3

11/18/2012 3 3 3 3 1 3 3 3

11/25/2012 3 3 2 3 1 3 2 2

12/2/2012 3 3 2 3 1 1 0 4

12/9/2012 3 3 3 3 1 2 3 3

12/16/2012 3 3 2 3 1 2 3 3

12/23/2012 2 2 1 1 0 2 1 2

12/30/2012 3 3 2 3 1 2 2 4

1/6/2013 3 3 3 3 1 3 3 3

1/13/2013 3 3 3 3 1 3 3 2

1/20/2013 3 3 3 3 1 3 3 2

1/27/2013 3 3 2 2 1 2 2 3