I€¦ · Web viewA Summary of Fisheries Research In The Lower Stanislaus River. Screw trap used to catch juvenile salmonids near Oakdale. Stanislaus River Fish Group

Initial Working Document 10 March 2004

Working DraftA Summary of Fisheries Research

In The Lower Stanislaus River

Screw trap used to catch juvenile salmonids near Oakdale

Stanislaus River Fish Group10 March 2004


1 INTRODUCTION 22 SUMMARY OF INFORMATION FOR SALMONID POPULATIONS WITHIN THE STANISLAUS RIVER 3

2.1 FALL-RUN CHINOOK SALMON 32.1.1 Fall-run Chinook Salmon Population Trends 32.1.2 Fall-run Chinook Salmon Life History 72.1.3 Fall-run Chinook Salmon Adult Upstream Migration 8

Fall-run Chinook Adult Upstream Migration Requirements 8Existing Stanislaus River Conditions and Effects on Fall-run Chinook Adult Upstream Migration 10

Water Temperature and Fall-run Chinook Adult Upstream Migration. 10Passage and Fall-run Chinook Adult Upstream Migration. 12Poaching and Fall-run Chinook Adult Upstream Migration. 12

2.1.4 Fall-run Chinook Salmon Spawning 13Fall-run Chinook Spawning Requirements 13Existing Stanislaus River Conditions and Effects on Fall-run Chinook Spawning 13

Fall-run Chinook Spawning Habitat Distribution. 15Fall-run Chinook Preferred Spawning Areas. 15Armoring and Embeddedness and Fall-run Chinook Salmon Spawning. 16Turbidity and Fall-run Chinook Spawning. 17

2.1.5 Fall-run Chinook Salmon Incubation and Emergence 17Fall-run Chinook Incubation and Emergence Requirements 17Existing Stanislaus River Conditions and Effects on Fall-run Chinook Incubation and Emergence 18

Fines and Dissolved Oxygen and Fall-run Chinook Incubation and Emergence. 18Streamflow and Fall-run Chinook Incubation and Emergence. 19Water Temperature and Fall-run Chinook Incubation and Emergence. 19

2.1.6 Fall-run Chinook Salmon Juvenile Rearing 19Fall-run Chinook Juvenile Rearing Requirements 19

Fall-run Chinook Juvenile Rearing Distribution. 22Streamflow and Fall-run Chinook Juvenile Rearing. 22Dissolved Oxygen and Fall-run Chinook Juvenile Rearing. 24Disease and Fall-run Chinook Juvenile Rearing. 31Contaminants and Fall-run Chinook Juvenile Rearing. 32Unscreened Diversions and Fall-run Chinook Juvenile Rearing. 35

Juvenile Fall-run Chinook Migration Requirements 36Existing Stanislaus River Conditions and Effects on Juvenile Fall-run Chinook Migration

37Streamflow and Juvenile Fall-run Chinook Migration. 37Water Temperature and Juvenile Fall-run Chinook Migration. 40Dissolved Oxygen, Predation, Disease, Contaminants, and Unscreened Diversions and Fall-run Juvenile Chinook Migration. 41

2.2 SPRING-RUN CHINOOK SALMON 412.2.2 Spring-run Chinook Salmon Life History 422.2.3 Spring-run Chinook Salmon Adult Upstream Migration 43

Spring-run Chinook Adult Upstream Migration Requirements 43Existing Stanislaus River Conditions and Effects on Spring-run Chinook Adult Upstream Migration 43

0


Streamflow and Spring-run Chinook Adult Upstream Migration. 43Water Temperature and Spring-run Chinook Adult Upstream Migration. 43Dissolved Oxygen and Spring-run Chinook Adult Upstream Migration. 43Poaching and Spring-run Chinook Adult Upstream Migration. 44

2.2.4 Spring-run Chinook Salmon Adult Holding Habitat 44Spring-run Chinook Adult Holding Requirements 44Existing Stanislaus River Conditions and Effects on Spring-run Chinook Adult Holding45

Streamflow and Spring-run Chinook Adult Holding. 45Water Temperature and Spring-run Chinook Adult Holding. 45Dissolved Oxygen and Spring-run Chinook Adult Holding. 46

2.2.5 Spring-run Chinook Salmon Spawning 46Spring-run Chinook Spawning Requirements 46

Spawning Habitat Distribution. 46Preferred Spawning Areas. 47Armoring and Embeddedness, and Turbidity. 47

2.2.6 Spring-run Chinook Salmon Incubation and Emergence 48Spring-run Chinook and Emergence Requirements 48

Streamflow and Spring-run Chinook Incubation and Emergence. 48Water Temperature and Spring-run Chinook Incubation and Incubation Habitat.

48Turbidity and Spring-run Chinook Incubation and Incubation Habitat. 49

2.2.7 Spring-run Chinook Salmon Juvenile Rearing 49Spring-run Chinook Juvenile Rearing Requirements 49Existing Stanislaus River Conditions and Effects on Spring-run Chinook Juvenile Rearing and Rearing Habitat 49

Water Temperature and Spring-run Chinook Juvenile Rearing. 49Streamflow, Dissolved Oxygen, Predation, Disease, Food Availability, Contaminants, and Unscreened Diversions and Spring-run Chinook Salmon Juvenile Rearing. 49

2.2.8 Spring-run Chinook Salmon Juvenile Migration 50Juvenile Spring-run Chinook Migration Requirements 50Existing Stanislaus River Conditions and Effects on Juvenile Fall-run Chinook Migration

50Water Temperature and Spring-run Chinook Juvenile Migration. 50Streamflow, Dissolved Oxygen, Predation, Disease, Contaminants, and Unscreened Diversions and Spring-run Chinook Migration. 50

2.3 STEELHEAD 502.3.1 Steelhead Population Trends 502.3.2 Steelhead Life History 532.3.3 Steelhead Adult Upstream Migration 54

Steelhead Adult Upstream Migration Requirements 54Existing Stanislaus River Conditions and Effects on Steelhead Adult Upstream Migration

54Streamflow and Steelhead Adult Upstream Migration. 55Dissolved Oxygen and Steelhead Adult Upstream Migration. 55Instream Harvest and Steelhead Adult Upstream Migration. 56Poaching and Steelhead Adult Upstream Migration. 56

2.3.4 Steelhead Spawning and Spawning Habitat 57

1


Steelhead Spawning and Spawning Habitat Requirements 57Existing Stanislaus River Conditions and Effects on Steelhead Spawning and Spawning Habitat 57

Steelhead Spawning Habitat Distribution. 57Steelhead Preferred Spawning Areas. 58Armoring and Embeddedness and Turbidity and Steelhead Spawning. 58

2.3.5 Steelhead Incubation and Emergence 58Steelhead Incubation and Emergence Requirements 58Existing Stanislaus River Conditions and Effects on Steelhead Incubation and Emergence

58Fines, Dissolved Oxygen, and Streamflow and Steelhead Incubation and Emergence. 58

2.3.6 Steelhead Juvenile Rearing 59Steelhead Juvenile Rearing Requirements 59Existing Stanislaus River Conditions and Effects on Steelhead Juvenile Rearing 59

Distribution of Steelhead Juvenile Rearing. 59Streamflow and Steelhead Juvenile Rearing. 60Dissolved Oxygen, Predation, Disease, Contaminants, and Unscreened Diversions and Steelhead Juvenile Rearing. 60Food Availability and Steelhead Juvenile Rearing. 61

2.3.7 Steelhead Juvenile Migration 61Dissolved Oxygen, Predation, Disease, Contaminants, and Unscreened Diversions and Steelhead Juvenile Migration. 62

3 SUMMARY OF INFORMATION FOR STANISLAUS RIVER SALMONID POPULATIONS OUTSIDE OF THE STANISLAUS RIVER (I.E., DELTA AND OCEAN)

633.1 ADULT CHINOOK SALMON AND STEELHEAD IN THE DELTA 63

3.1.2 Adult Chinook Salmon and Steelhead Migration through the Delta 63Chinook Salmon and Steelhead Adult Upstream Migration Requirements 63Existing Delta Conditions and Effects on Chinook Salmon and Steelhead Adult Upstream Migration 63

Delta Flow Conditions and Chinook Salmon and Steelhead Adult Upstream Migration. 63Dissolved Oxygen and Water Temperature, and Chinook Salmon and Steelhead Adult Upstream Migration. 67Passage and Chinook Salmon and Steelhead Adult Upstream Migration. 71

3.2 JUVENILE CHINOOK SALMON IN THE DELTA 713.2.2 Juvenile Chinook Rearing and Migration in the Delta 71

Juvenile Chinook Salmon Estuarine Rearing and Migration Requirements 71Existing Delta Conditions and Effects on Juvenile Chinook Salmon Rearing and Migration 71

Delta Flow Conditions and Juvenile Chinook Salmon Rearing and Migration. 73Water Temperature and Juvenile Chinook Salmon Rearing and Migration. 77Predation and Juvenile Chinook Salmon Rearing and Migration. 79Delta Exports and Juvenile Chinook Salmon Rearing and Migration. 80Head of the Old River Barrier and Juvenile Chinook Salmon Rearing and Migration. 81

3.3 OCEAN SURVIVAL 82

2


3.3.1. Ocean Climate 823.3.2 Ocean Harvest 83

4. LITERATURE CITED 845. PERSONAL COMMUNICATIONS 98

3


LIST OF FIGURES

Figure 1. Lower Stanislaus River between New Melones Reservoir and the confluence with the San Joaquin River. The larger black dots indicate towns, and the smaller green dots with abbreviated labels show the approximate locations of the Stanislaus River Parks that are owned and managed by the U.S. Army Corps of Engineers. These recreation areas include Two-Mile Bar (TMB), Knights Ferry (KF), Lovers Leap (LL), Horseshoe Road (HR), Honolulu Bar (HB), Buttonbush (BB), Orange Blossom (OB), Valley Oak (VO), Oakdale Recreational Park (OR), Riverbank (RB), Jacob Meyers (JM), McHenry Avenue (MHA), Ripon (RP), Mohler Road (MR), and River’s End (RE). The location of Caswell Memorial State Park is also shown..........................................................................................................2

Figure 2. California Department of Fish and Game estimates of escapement of fall-run Chinook salmon in the lower Stanislaus River from 1947 to 2002. There are no estimates for 1950, 1977, and 1982, and the 1996 estimate was omitted because no tagged carcasses were recovered to obtain an accurate estimate.................................................................................4

Figure 3. The relationship between the number of fall-run Chinook salmon recruits to the lower Stanislaus River and Age 3 equivalent stock over three ranges of flow in the San Joaquin River at Vernalis between April 15 and May 15 during years 1952 to 2000. Data labels indicate the year when juvenile fish outmigrated....................................................................5

Figure 4. The relationship between the number of fall-run Chinook salmon recruits/spawner to the lower Stanislaus River and the average flow in the San Joaquin River at Vernalis between 15 April and 15 May from 1952 to 2000. The estimated number of recruits/spawner assumes that recruit abundance is unaffected by spawner abundance after spawner abundance exceeds 2,000 Age 3 equivalent fish. Recruit/spawner estimates are not shown for those with spawner abundance less than 493 Age 3 equivalent fish......................6

Figure 5. The relationship between the estimated number of juvenile fall-run Chinook salmon passing the Oakdale screw trap in 1996 and from 1998 through 2003, and the number of spawners which produced them in 1995 and from 1997 to 2002. The 1996 juvenile passage estimate was adjusted for late initiation of sampling based on the proportion of the total number of juveniles estimated to have passed Oakdale in 2000 (year of most similar flow) prior to February 1...................................................................................................................7

Figure 6. Daily average water temperatures in the San Joaquin (RRI= Rough and Ready Island at RM 37.7 and MSD= Mossdale at RM 56.3) and Stanislaus (RIP= Ripon at RM 15.8 and SRW= Stanislaus River Weir at RM 31) Rivers, September 1-October 15, 2003. Note: adult passage first observed at weir on September 19 with peak passage of 716 fish occurring on October 9.................................................................................................................................9

Figure 7. Average maximum daily water temperature in the Stanislaus River at Knights Ferry, Oakdale, and Caswell from 1998 through 2003, and adult Chinook requirements...............11

Figure 8. Dissolved oxygen levels in the Stanislaus River at Ripon from 1999 through 2003. Average is the mean of all average values observed over the period of record for a particular date. Minimum is the mean of all minimum daily values observed over the period of record for each particular date. Maximum is the mean of all maximum daily values observed over the period of record for each particular date..........................................................................12

Figure 9. Fall-run Chinook salmon redd density relative to the distance below Goodwin Dam in fall 1994, 1995, 1996, and 1998. The regressions for these relationships are shown as the four lines................................................................................................................................16

4


Figure 10. Average maximum daily water temperatures and juvenile Chinook rearing requirements at Caswell, Oakdale, and Knight’s Ferry, 1998-2003. Preferred range encompasses fry (50°F to 55°F; Boles and others 1988; Rich 1997; Seymour 1956) and fingerlings (55°F to 60°F; Rich 1997); chronic stress threshold (CDFG 2002a); lethal limit (Baker and others 1995).........................................................................................................23

Figure 11. Maximum mean daily water temperature at Caswell State Park in the lower Stanislaus River during above-normal water years (1998, 1999, and 2000,), and dry water years (2001, 2002, and 2003).........................................................................................................24

Figure 12. The lowest river mile achieved by radio-tagged smolts in 1999..................................26Figure 13. Frequency of predator species and juvenile Chinook salmon in main channel and

pond/backwater habitats near the Oakdale Recreation Park and McHenry Park in the lower Stanislaus River in May and June 1999 (SPC, unpublished data).........................................27

Figure 14. Maximum daily turbidity (Nephelometric Turbidity Units) recorded at the screw trap at Caswell State Park in above-normal water years (1998 and 2000), and in dry water years (2001, 2002 and 2003; SPC 2003).........................................................................................28

Figure 15. Relationship of juvenile Chinook weight to fork length based on individuals captured in the Oakdale and Caswell screw traps in 1999, 2001, 2002, and 2003. Weight data are not available from 2000, nor from years prior to 1999................................................................34

Figure 16. Estimated annual biomass of juvenile Chinook salmon passing Oakdale and Caswell during 1999, 2001, 2002 and 2003. Weight data are not available from 2000, nor from years prior to 1999 to estimate biomass..........................................................................................35

Figure 17. Absolute survival of juvenile Merced River Hatchery Chinook salmon migrating in the lower Stanislaus River between Knights Ferry and the confluence with the San Joaquin River relative to flow releases from Goodwin Dam..............................................................38

Figure 18. Estimated survival of naturally produced juvenile Chinook salmon migrating in the lower Stanislaus River between Oakdale and Caswell State Park based on the differences in estimated screw-trap passage estimates.................................................................................39

Figure 19. Absolute survival of juvenile Merced River Hatchery Chinook salmon migrating in the lower Stanislaus River between Knights Ferry and the confluence with the San Joaquin River relative to the mean daily water temperature at Ripon................................................40

Figure 20. Individual lengths of O. mykiss captured in the Oakdale and Caswell rotary screw traps from 1995 through 2003...............................................................................................52

Figure 21. Annual estimated O. mykiss passage at Oakdale from 1996 through 2003. Passage estimates are catch expanded for the estimated proportion of flow sampled by the trap......53

Figure 22. Average maximum daily temperatures at Caswell, Oakdale, and Knights Ferry, 1998-2003, and adult steelhead requirements.................................................................................55

Figure 23. Estimated percent of adult CWT Chinook salmon that were reared at the Merced River Hatchery, released in the San Joaquin basin as juvenile salmon, and subsequently strayed to the Sacramento River and eastside tributary basins to spawn relative to the average ratio of Delta export rates at the CVP and SWP pumping facilities to San Joaquin River flow rates at Vernalis between October 15 and 21, 1983 to 1996...............................65

Figure 24. The ratio of combined exports at the CVP and SWP facilities during a 10-day pulse flow period in mid-October from 1993 to 2002....................................................................66

Figure 25. Mean monthly percentage of San Joaquin River flow at Vernalis that was exported at the State Water Project and the Federal Water Project during February through March from 1990 to 2002. Data collected during wet years and above normal years are indicated with hourglass and oval symbols, respectively..............................................................................67

5


Figure 26. Minimum DO concentrations measured at hourly intervals at the Department of Water Resources’ Burns Cut Off Road monitoring station during the adult spring-run Chinook salmon migration period from 1990 to 2002. Data collected during wet years and above normal years are indicated with hourglass and oval symbols, respectively..........................68

Figure 27. Hourly dissolved oxygen measurements at the Department of Water Resources’ Burns Cut Off Road monitoring station in 1992 and 2002..............................................................69

Figure 28. Mean monthly water temperature measured at hourly intervals at the Department of Water Resources’ Burns Cut Off Road monitoring station from 1990 to 2002. Data collected during wet years and above normal years are indicated with hourglass and oval symbols, respectively.............................................................................................................70

Figure 29. The estimated number of fry, parr, and smolt-sized juvenile Chinook salmon passing the screw trap at Oakdale in the lower Stanislaus River. Sampling during 1998 and 1999 began in mid February and so most, but not all fry, were probably captured during these years.......................................................................................................................................72

Figure 30. Map of Delta release and recovery locations.........................................................74Figure 31. The relationship between the number of fall-run Chinook salmon recruits/spawner to

the lower Stanislaus River and average ratio of combined exports at the SWP and CVP pumping facilities in the Delta between 15 April and 15 May from 1952 to 2000. The estimated number of recruits/spawner assumes that recruit abundance is unaffected by spawner abundance after spawner abundance exceeds 2,000 Age 3 equivalent fish. Recruit/spawner estimates are not shown for those with spawner abundance less than 493 Age 3 equivalent fish.............................................................................................................77

Figure 32. The absolute survival of CWT juvenile salmon from the Merced River Hatchery released at Mossdale with the HORB installed or at Dos Reis in April or early May from 1996 to 2002 relative to the mean daily water temperature in the Stockton ship channel near Burns Cutoff Road.................................................................................................................78

Figure 33. The absolute survival of CWT juvenile salmon from the Merced River Hatchery released at Mossdale with the HORB installed or at Dos Reis in April or early May from 1996 to 2002 relative to the mean DO concentration in the Stockton ship channel near Burns Cutoff Road.................................................................................................................79

6


LIST OF TABLES

Table 1. The number and size of fish collected during electrofishing surveys in captured mine ponds at the Oakdale Recreational Park and McHenry Park and in the river’s main channel 1-2 miles upstream and downstream of the Oakdale Recreation Pond in May and June 1999 (SPC, unpublished data)........................................................................................................26

Table 2. EA Engineering, Science, and Technology predation studies in the lower Tuolumne River in 1989 and 1990 (EA 1992)........................................................................................30

Table 3. The number of tagged juvenile Chinook salmon released at the various study sites in the Delta in 1991, the number recovered in the ocean fisheries, and the survival index used to estimate absolute survival and mortality rates.......................................................................74

Table 4. Pearson correlation coefficients (r) and probabilities (P) for the relationships between the number of recruits-per-spawner of fall-run Chinook salmon in the Stanislaus River and flows at Vernalis and flow releases from Goodwin Dam from December through June and during the April 15 to May 15 VAMP period for 35 observations between 1952 and 2000.76

Table 5. Number and mean fork length of largemouth bass, smallmouth bass, and striped bass per kilometer that were collected during CDFG electrofishing surveys in the Sacramento-San Joaquin Delta, 1980 to 1983. The sampling sites in each region of the Delta are shown in Figure 1 of Schaffter (2000)..............................................................................................80

7


LIST OF ACRONYMS AND ABBREVIATIONS

AFRP Anadromous Fish Restoration ProgramBKD bacterial kidney diseaseBB ButtonbushBO Biological OpinionCALFED California Bay-Delta AuthorityCDEC California Data Exchange CenterCDFG California Department of Fish and Gamecfs cubic-feet-per-secondCMC Carl Mesick Consultantscm/hour centimeters per hourCRRF California Rivers Restoration FundCVP Central Valley Project pumping facilities at TracyCVPIA Central Valley Project Improvement ActCWT coded-wire tagCVI Central Valley IndexD-1641 State Water Resources Control Board Decision #1641DO dissolved oxygenDWR California Department of Water ResourcesEA Engineering EA Engineering, Science, and Technology, Inc.ESU evolutionary significant unitF FahrenheitFL Fork lengthg gramsHORB Head of the Old River BarrierHR Horseshoe Rd.HB Honolulu BarIEP Interagency Ecological ProgramIFIM Instream flow incremental methodologyJM Jacob MeyersKF Knights FerryKFGRP Knights Ferry Gravel Replenishment ProjectLL Lovers Leapmm millimetermg/L milligrams per literMHA McHenry AvenueMR Mohler Rd.NMIPO New Melones Interim Plan of OperationNOAA Fisheries National Marine Fisheries ServiceOB Orange BlossomOR Oakdale Recreational ParkPKD proliferative kidney diseasep Pearson correlation probabilitiesr Pearson correlation coefficientsRM rivermileRB RiverbankRP Ripon

8


RE River’s EndSJRGA San Joaquin River Group AuthoritySPC S.P. Cramer & Associates, Inc.SRA shaded riverine aquaticSRFG Stanislaus River Fish GroupSSR Off Site Release and Straying Subcommittee ReportSWP State Water Project pumping facilities in the DeltaSWRCB State Water Resources Control BoardTMB Two-Mile BarUSBR U.S. Bureau of ReclamationUSFWS U.S. Fish and Wildlife ServiceUSGS U.S. Geological SurveyVAMP Vernalis Adaptive Management ProgramVO Valley Oak

LIST OF RIVER MILES FOR FREQUENTLY DISCUSSED LOCATIONS

Stanislaus River

Goodwin Dam RM 58.4Two-Mile Bar RM 56.5Knights Ferry RM 54Frymire Ranch RM 53.4Lovers’ Leap RM 53.3Willm’s Pond RM 51.8Honolulu Bar RM 49.6Buttonbush Park RM 48Orange Blossom Bridge RM 46.9Kerr Park RM 43.5Oakdale Rotary Screw Trap RM 40.1Oakdale Recreation Area Pond RM 39.8Jacob Meyers Park/Riverbank RM 33Ripon RM 15.8Caswell RM 8.6

San Joaquin River

Mouth of Stanislaus River RM 74.9Vernalis RM 72.3Mossdale RM 54

9


1 INTRODUCTION

The Stanislaus River Fish Group is developing a restoration plan (Plan) to restore habitat for Chinook salmon (formally King salmon; Oncorhynchus tshawytscha) and steelhead (O. mykiss) in the lower Stanislaus River that is currently accessible to anadromous salmonids which is the 58.3 mile reach between Goodwin Dam and the confluence with the San Joaquin River (Figure1). The centerpiece of the Plan is a conceptual model that describes potential factors contributing to declines in Stanislaus River salmonid abundance. The conceptual model is based on the results of fishery studies and monitoring conducted in the Stanislaus River and in other Central Valley rivers over the last several decades and the combined experience of the SRFG members.

This summary report was prepared to assist in development of the Plan’s conceptual model and to provide a synthesis of existing knowledge regarding Stanislaus River fall-run Chinook salmon, spring-run Chinook salmon, and steelhead. Specifically, the information identified in this report was used to help identify the following: (1) primary factors that have likely contributed substantially to the decline of salmonids and their habitat in the Stanislaus River; (2) habitat restoration opportunities that, if implemented, should increase the abundance of salmon and steelhead; and (3) data gaps where research is needed to improve the effectiveness of restoration and fisheries management.

Figure 1. Lower Stanislaus River between New Melones Reservoir and the confluence with the San Joaquin River. The larger black dots indicate towns, and the smaller green dots with abbreviated labels show the approximate locations of the Stanislaus River Parks that are owned and managed by the U.S. Army Corps of Engineers. These recreation areas include Two-Mile Bar (TMB), Knights Ferry (KF), Lovers Leap (LL), Horseshoe Road (HR), Honolulu Bar (HB), Buttonbush (BB), Orange Blossom (OB), Valley Oak (VO), Oakdale Recreational Park (OR), Riverbank (RB), Jacob Meyers (JM), McHenry Avenue (MHA), Ripon (RP), Mohler Road (MR), and River’s End (RE). The location of Caswell Memorial State Park is also shown.

10


2 SUMMARY OF INFORMATION FOR SALMONID POPULATIONS WITHIN THE STANISLAUS RIVER

Fishery studies and monitoring, primarily focused on fall-run Chinook salmon, have been conducted over the last several decades in the Stanislaus River. In more recent years, steelhead have been added as target species for study. Studies have indicated that Stanislaus River salmonid populations are impacted by a number of factors within the river, as well as factors in the Sacramento/San Joaquin Delta, San Francisco Bay Estuary, and ocean. The following provides a summary of the findings of these studies as they relate to Stanislaus River populations of fall and spring-run Chinook salmon, and steelhead.

2.1 FALL-RUN CHINOOK SALMON

2.1.1 Fall-run Chinook Salmon Population Trends

Fall-run Chinook salmon escapement (i.e., number of adults returning to their natal stream to spawn) in the Stanislaus River has fluctuated substantially due to a variety of factors, including harvest, climate, flow, and habitat degradation (Figure 2). Escapement was usually low except following extended periods of spring flooding, as occurred in 1952, 1958, 1967, 1969, 1982, 1983, 1995, and 1998. Peaks in escapement usually occurred two years after spring flooding when there were at least 500 spawning adults the year prior to the flood. One possible explanation for this trend is that the conditions that occur during flooding improve the survival of juvenile salmon as they migrate toward the ocean. Presumably as a result of the improved juvenile survival during floods, a greater number of adult fish return to spawn in the Stanislaus River two years later.

11


0

10,000

20,000

30,000

40,000

Esca

pem

ent

19471952

19571962

19671978

19771982

19871992

19972002

Year

Stanislaus River Escapement

X X X

Figure 2. California Department of Fish and Game estimates of escapement of fall-run Chinook salmon in the lower Stanislaus River from 1947 to 2002. There are no estimates for 1950, 1977, and 1982, and the 1996 estimate was omitted because no tagged carcasses were recovered to obtain an accurate estimate.

In order to assess the relationship between flow and juvenile survival, recruitment and stock were calculated then evaluated over a range of flows observed in the San Joaquin River approximately 2.6 river miles below the mouth of the Stanislaus River at Vernalis (RM 72.3) between April 15 and May 15 (peak of juvenile salmon outmigration through the Delta) each year. For this analysis, recruitment was defined as the number of salmon within a given cohort (i.e., juveniles produced within the same year) surviving to Age 2. The calculations for estimating recruitment required that escapement estimates were first segregated into abundance estimates for Ages 2, 3, 4, and 5 fish, then summed with the estimated sport and commercial harvest of each age class, and subsequently adjusted for known cycles of ocean productivity and climate. These methods are described in detail in Appendix 1.

Stock was defined as the number of equivalent Age 3 spawners, and is essentially the total escapement segregated by cohort and standardized for Age 3 fecundity. These methods are described in detail in Appendix 1. Age 3 equivalent spawners were calculated using the following formula:

Stock = 0.38 * Age 2’s + Age 3’s + 1.2 * Age 4’s + 1.4 * Age 5’s

12


Results of this analysis suggest that recruitment is correlated with both stock and streamflow at Vernalis and is relatively the same for flows in the manageable ranges between 1,750-4,000 cfs and 5,000-11,000 cfs, but changes at flood flows above 18,000 cfs (Figure 3). Recruitment is higher under flood flows above 18,000 cfs than under flows in the managed range from 1,750-11,000 cfs. The stock-recruitment relationship for the lower Stanislaus River appears to be similar to the relationships described for other salmon populations by Beverton-Holt (Ricker 1975), although the errors associated with the estimates of Stanislaus River recruitment may be too large to evaluate the exact shape of the curves (Appendix 1). This relationship suggests that within a particular flow range, recruitment rapidly increases up to 1,000 to 2,000 spawners and then remains relatively flat or slowly increases as the number of spawners exceeds 2,000 Age 3 equivalent fish (Figure 4).

0

15,000

30,000

45,000

60,000

Re

cru

its

0 2,000 4,000 6,000 8,000 10,000 12,000 14,000Stock

52

58

65

67 69

8283

86

95 98

56

6399

00 5362 70

71737579

84

85

878893

94

> 18,000 cfs 5,000 - 11,000 cfs 1,750 - 4,000 cfs

Stanislaus River Stock and Recruits

Figure 3. The relationship between the number of fall-run Chinook salmon recruits to the lower Stanislaus River and Age 3 equivalent stock over three ranges of flow in the San Joaquin River at Vernalis between April 15 and May 15 during years 1952 to 2000. Data labels indicate the year when juvenile fish outmigrated.

13


0

5

10

15

20

25

30

Rec

ruits

/Spa

wne

r

0 5,000 10,000 15,000 20,000 25,000 30,000 35,000Vernalis Flows (cfs)

52

535556

57

58

596061

62

65

66

67

68

69

70

71ERR

73 74757677

8283

8485

86

87888990

9194

95

9697

98

9900

Pre 1994 Post 1994

Stanislaus River Recruits Per Spawnerand San Joaquin River Flow

Figure 4. The relationship between the number of fall-run Chinook salmon recruits/spawner to the lower Stanislaus River and the average flow in the San Joaquin River at Vernalis between 15 April and 15 May from 1952 to 2000. The estimated number of recruits/spawner assumes that recruit abundance is unaffected by spawner abundance after spawner abundance exceeds 2,000 Age 3 equivalent fish. Recruit/spawner estimates are not shown for those with spawner abundance less than 493 Age 3 equivalent fish.

A similar relationship has also been observed between the number of spawners and the total estimated number of juveniles passing a screw trap at Oakdale (RM 40.1) in 1996 and 1998 to 2003 (Figure 5; S. P. Cramer and Associates, Inc. [SPC] 2003). From the limited amount of data available, it appears that the number of juveniles rapidly increases with an initial increase in the number of spawners, but then remains relatively flat as the carrying capacity (either for spawners or juveniles) is approached and exceeded. The estimates between 2000 and 2003 are higher than previous years may have been affected by the Knights Ferry Gravel Replenishment Project (KFGRP), which restored spawning and rearing habitat at 18 sites between Two-Mile Bar and the Oakdale Recreation Area in late summer 1999. The availability of spawning and rearing habitat in the highly used reach between Two-Mile Bar and Willms Pond was nearly doubled by the KFGRP and all of these sites were immediately well used by spawning (CMC 2002a and 2002b) and rearing (Fisheries Foundation 2002) fall-run Chinook salmon. However, the years of highest escapement were also dry years, and the years of lowest escapement and were wet years which confounds the interpretation of this relationship.

14


Combined, these relationships for the Stanislaus River appear to indicate that the carrying capacity is between 1,000 and 3,000 Age 3 equivalent spawners, or 1.5 to 2.0 million juveniles. This is well below the Central Valley Project Improvement Act (CVPIA) production goal of approximately 20,000 fall-run Chinook which would result in 10,000 or more spawners escaping to the Stanislaus River, assuming harvest is 50% or less.

500,000

1,000,000

1,500,000

2,000,000

Ju

ve

nil

e P

as

sa

ge

Es

tim

ate

0 3,000 6,000 9,000Stock

1996

1998

1999

2000

2001

2002

2003

Pre-KFGRP Post-KFGRP

Stock and Juvenile Passage

Figure 5. The relationship between the estimated number of juvenile fall-run Chinook salmon passing the Oakdale screw trap in 1996 and from 1998 through 2003, and the number of spawners which produced them in 1995 and from 1997 to 2002. The 1996 juvenile passage estimate was adjusted for late initiation of sampling based on the proportion of the total number of juveniles estimated to have passed Oakdale in 2000 (year of most similar flow) prior to February 1.

2.1.2 Fall-run Chinook Salmon Life History

Pacific salmon have adopted a variety of life history strategies including varying juvenile rearing and migration patterns to capitalize on diverse habitat and environmental conditions associated with freshwater river systems. Furthermore, Chinook salmon exhibit the most significant life history diversity within salmon populations throughout the Pacific Northwest (Ricker 1972; Healey 1986, 1991).

The first fall-run adult migrants entering the Stanislaus River are typically observed in late September (Guignard, personal communication, 2003; SPC unpublished data) Similar observations have been made on the Mokelumne River (Workman 2002). A small fraction of

15


these early arrivals may be spring-run, however, the majority are believed to be fall-run (Guignard, personal communication, 2003). The majority of spawning occurs from October through December. Eggs are laid in nests called redds, and need cool water and good water flow (to supply oxygen) to survive. Once spawning is completed, adult Chinook salmon die.

Young salmon typically begin to emerge from the redds in mid-December and have an average forklength of approximately 35 mm. Fry (<45 mm) and parr (45 mm to 79 mm) may spend time rearing within riverine and/or estuarine habitats including natal tributaries, the San Joaquin River, non-natal tributaries to the San Joaquin River, and the Delta. In general, emigrating juveniles that are younger (i.e., smaller) reside longer in estuaries such as the Delta (Kjelson and others 1982; Levy and Northcote 1982; Healey 1991). The brackish water areas in estuaries moderate the physiological stress that occurs during parr-smolt transitions. In the Stanislaus River, the majority (>95%) of fall-run Chinook juveniles typically emigrate from the river and enter the San Joaquin River and Delta as fry, parr, or smolts from January through May. Although fry and parr can enter the Delta as early as January and as late as June, their length of residency within the Delta is unknown but probably lessens as the season progresses into the late spring months (CDFG 1998a).

After a brief, or sometimes relatively extended, residence time within estuarine areas, juvenile salmon continue their migration to sea where they spend anywhere from one to five years maturing (average 3-4 years) before returning to their natal streams to spawn (Healey 1991).

2.1.3 Fall-run Chinook Salmon Adult Upstream Migration

Fall-run Chinook Adult Upstream Migration Requirements

Adult migration requirements for fall-run Chinook include suitable water temperatures and DO levels, and adequate passage to the spawning grounds (i.e., no physical barriers). Unfortunately, the thermal requirements of adult migrating Chinook salmon in the Stanislaus River are unknown due to the lack of thermal studies conducted with locally adapted fish and limited studies conducted elsewhere within the San Joaquin Basin and California. Salmon within the San Joaquin Basin have adapted to conditions where temperatures are consistently higher throughout the year and are more prone to fluctuate both within and between years than temperatures found in more northern latitudes.

In the absence of site specific data, Central Valley Chinook salmon temperature preferences and requirements have typically been based on temperature studies conducted primarily with hatchery fish in the Pacific Northwest which may result in temperature ranges that are not appropriate for these southernmost stocks. Based on the available literature, the preferred temperature range for Chinook salmon completing their upstream migration has been identified as 38°F to 56°F (Bell 1991)1. Adult fall-run Chinook have been observed to begin experiencing physiological stress when exposed to temperatures in the range of between 59°F to 68°F for prolonged periods (Marine and Cech 1992) and have exhibited poor egg viability when held in 1 Note: temperature requirements given for all lifestages of Chinook salmon are based primarily on studies conducted outside of the San Joaquin Basin and are often conducted within laboratory conditions using hatchery fish, so “wild” salmon within the San Joaquin Basin may have slightly higher temperature preferences and/or tolerances than those used within this report. Higher temperature preferences and/or tolerances may be due to adaptation of San Joaquin salmon to naturally higher temperature conditions existing at the southernmost extent of their range and/or due to distinctive differences between “wild” and hatchery fish.

16


hatcheries at temperatures greater than 60°F prior to spawning (Hinze 1959). Incipient lethal temperature2 has been identified as 69.8°F3 (Houston 1982; Coutant 1970) while sustained water temperatures above 80.6°F have been found to be lethal to adults (Cramer and Hammack 1952; CDFG 1998b). Hallock and others (1970) observed that adult Chinook migration in the lower San Joaquin River ceased at temperatures above 70°F3, then resumed when temperatures decreased to 65°F.

These previously identified thermal tolerances and blockage temperatures do not appear to reflect fish survival and behavior observed under “natural” field conditions within the Stanislaus River. For example, although incipient lethal temperatures have been identified as 69.8°F (Houston 1982; Coutant 1970) and radio tracking studies performed in the lower San Joaquin/Delta (Hallock and others 1970) and elsewhere such as Washington (Bumgarner and others 1997) and Idaho (Stabler 1981) have indicted that adult upstream migration becomes blocked at about 70°F, recent observations of adult salmon passage in the Stanislaus River during a demonstration weir project in 2003 indicate that fish had to migrate for prolonged periods at average daily water temperatures above 70°F (Figure 6) in the Delta and lower San Joaquin to reach the weir site.

40

50

60

70

80

Tem

pera

ture

(F)

01-Sep16-Sep

01-Oct16-Oct

31-Oct15-Nov

30-Nov15-Dec

30-Dec

SRW RIP MSD RRI

Water Temperature in the San Joaquinand Stanislaus Rivers, 2003

Figure 6. Daily average water temperatures in the San Joaquin (RRI= Rough and Ready Island at RM 37.7 and MSD= Mossdale at RM 56.3) and Stanislaus (RIP= Ripon at RM 15.8 and SRW= Stanislaus River Weir at RM 31) Rivers, September 1-October 15, 2003. Note: adult passage first observed at weir on September 19 with peak passage of 716 fish occurring on October 9.

2 Incipient Lethal Temperature is the temperature needed to produce 50% mortality of fish which are acclimated to one temperature, then subjected instantaneously to another temperature.3 This value does not seem to apply to San Joaquin stocks since recent observations of adult salmon passage in the Stanislaus River during a demonstration weir project in 2003 indicate that fish had to migrate for prolonged periods at average daily water temperatures above 70°F.

17


These high temperature conditions in the Delta and lower San Joaquin exist each year during the early period of upstream migration, particularly September. However, adult salmon are apparently not impeded by these conditions as long as dissolved oxygen is sufficient. Although adult salmon are able to migrate at higher temperatures than previously expected, they may still be susceptible to pre-spawning reductions in egg viability when exposed to these higher, sub-lethal temperatures. Adult salmon exposure to high temperatures in the Delta and lower San Joaquin could decrease the likelihood that salmon returning to the Stanislaus River in September are able to appreciably contribute to production.

Due to the naturally warmer and fluctuating temperature conditions in the San Joaquin Basin, in conjunction with information obtained from more recent thermal studies conducted within the Central Valley, fall-run Chinook salmon within the Stanislaus River are anticipated to have higher thermal tolerances during some lifestages than those often cited from studies conducted in the Pacific Northwest. However, the actual temperature tolerances for adult migration in the San Joaquin basin are currently unknown.

Existing Stanislaus River Conditions and Effects on Fall-run Chinook Adult Upstream Migration

Based on the environmental and fishery data collected during various monitoring studies discussed in the following sections, it appears that fall-run Chinook adult upstream migration opportunities are suitable in the Stanislaus River.

Streamflow and Fall-run Chinook Adult Upstream Migration. Stanislaus River flows during most of the adult fall-run Chinook upstream migration period provide suitable water depths, velocities, and water temperatures for adult passage to existing spawning grounds. However, inadequate attraction flow conditions that may result in straying due to low DO in the Delta have been a concern (see Section 3.1.2, Existing Delta Conditions and Effects on Chinook Salmon and Steelhead Adult Upstream Migration). Since 1993, artificial flow pulses intended to reduce adult straying, commonly referred to as attraction pulses, have been provided during the fall. Attraction flows are typically sustained for 5-10 days during mid- to late October and vary in magnitude depending on the volume of water available according to the agency agreements identified in Chapter 3 of the Plan.

Water Temperature and Fall-run Chinook Adult Upstream Migration. Maximum daily water temperatures in the Stanislaus River have been monitored at Caswell (RM 8.6) since 1998. Temperatures are higher at this location compared to temperatures near actual spawning grounds, because the Caswell monitoring station is located about 15 miles downstream of the lowermost extent of the spawning reach. During the fall-run Chinook migration period, average maximum daily water temperatures (i.e., the average of maximum water temperature values recorded on a particular date for the period of record) at Caswell generally declined from approximately 70°F

18


in September to 50°F in December (These previously identified thermal tolerances and blockagetemperatures do not appear to reflect fish survival and behavior observed under “natural” fieldconditions within the Stanislaus River. For example, although incipient lethal temperatures havebeen identified as 69.8°F (Houston 1982; Coutant 1970) and radio tracking studies performed inthe lower San Joaquin/Delta (Hallock and others 1970) and elsewhere such as Washington(Bumgarner and others 1997) and Idaho (Stabler 1981) have indicted that adult upstreammigration becomes blocked at about 70°F, recent observations of adult salmon passage in theStanislaus River during a demonstration weir project in 2003 indicate that fish had to migrate forprolonged periods at average daily water temperatures above 70°F (Figure 6) in the Delta andlower San Joaquin to reach the weir site.In general, average maximum daily water temperatures exceed 65°F at Caswell during September which suggests that egg viability of early adult migrants traveling through the lower reaches could be reduced, potentially affecting less than 5% of the run. The potential for reduced egg viability during this period is not unique to the Stanislaus River. Temperatures throughout the Delta and lower reaches of other tributaries are similar at this time, so any salmon beginning their freshwater migration during the summer months are likely to experience some degree of reduced egg viability during their migration through the Delta and into at least the lower reaches of spawning tributaries. Temperatures in October through December are typically suitable at Caswell and are not likely to adversely affect egg viability and behavior of adult upstream migrants.

35

45

55

65

75

85

Te

mp

era

ture

(F

)

01-Jan03-Feb

07-Mar09-Apr

12-May14-Jun

17-Jul19-Aug

21-Sep24-Oct

26-Nov29-Dec

Knights Ferry Oakdale Caswell

Average Maximum Daily TemperatureAnd Adult Chinook Requirements

LethalLimit

Egg Viability Threshold

PreferredRange

Figure 7. Average maximum daily water temperature in the Stanislaus River at Knights Ferry, Oakdale, and Caswell from 1998 through 2003, and adult Chinook requirements.

19


Dissolved Oxygen and Fall-run Chinook Adult Upstream Migration. Studies conducted by Hallock and others (1970) determined that adult Chinook either delayed their upstream migration or strayed to the San Joaquin/Delta system when dissolved oxygen levels were lower than 5 mg/L. Since 1999, DO measurements have been recorded hourly at Ripon and have encompassed a range of water year types and corresponding flows (dry to wet years with low to high flows, respectively). The average minimum daily DO (i.e., the average of minimum DO values recorded on a particular date for the period of record) at Ripon generally ranged from 7 to 11, and never fell below 5 mg/L (Figure 8) indicating that DO in the Stanislaus River is not likely to be a problem for upstream migrants.

0

3

6

9

12

15

DO

at

RP

N (

mg

/L)

01-Jan03-Feb

07-Mar09-Apr

12-May14-Jun

17-Jul19-Aug

21-Sep24-Oct

26-Nov29-Dec

Average Maximum Average Average Minimum

Average, Minimum, and Maximum DOon the Stanislaus River, 1999-2003

Figure 8. Dissolved oxygen levels in the Stanislaus River at Ripon from 1999 through 2003. Average is the mean of all average values observed over the period of record for a particular date. Minimum is the mean of all minimum daily values observed over the period of record for each particular date. Maximum is the mean of all maximum daily values observed over the period of record for each particular date.

Passage and Fall-run Chinook Adult Upstream Migration. Goodwin Dam is the first impassable barrier in the Stanislaus River that fish traveling upstream from the San Joaquin River encounter. This dam prevents adult salmonids from entering the historically accessible upper river and headwater reaches. However, fall-run Chinook tend to use the lower reaches of rivers and apparently did not travel as far upstream as Goodwin Dam (RM 58.3) based on historic accounts of spawning activity which indicate that spawning occurred in a ten mile stretch below Knights Ferry (RM 54; Clark 1929). Currently, there are no physical passage barriers below Goodwin Dam to limit upstream passage of fall-run Chinook and flows are adequate for maintaining upstream passage opportunities once fish have entered the river.

Poaching and Fall-run Chinook Adult Upstream Migration. Under current California Department of Fish and Game (CDFG) fishing regulations for the Stanislaus River, no fishing is allowed from October 16 through December 31 which encompasses the majority of the fall-run

20


Chinook migration period, and there is a zero bag limit for salmon during the fishing season from January 1 through October 15. Although CDFG regulations limit the impacts of fishing on migrating salmon, CDFG has indicated that poaching (i.e., illegal harvest) of adult Chinook salmon in the Stanislaus River likely occurs and has been increasing during the last five years. However, no information is currently available regarding the extent of poaching and the magnitude of fall-run adult migrant loss due to poaching can not be estimated at this time.

Due to budget and staff constraints, CDFG wardens infrequently patrol the river from Goodwin Dam to the Orange Blossom Bridge. Most enforcement of the fishing regulations results from sport fisherman reporting violations to the CDFG wardens using the Cal Tip hotline (Tony Spada, personal communication, 2002). However, poaching and other violations are virtually unchecked between October 16 to December 31 when the river is closed to fishing and sport anglers are not present on the river. Moreover, regulations allowing bait fishing downstream of the Highway 120 Bridge is a frequent excuse for illegally using bait upstream of this section. These problems might be remedied by (1) providing funding to increase the patrol of game wardens on the river, especially from October 16 to December 31, when the river is closed to fishing, and (2) implementing new regulations below Highway 120 to match the regulations in place above Highway 120 where fishermen may only use artificial lures with barbless hooks.

2.1.4 Fall-run Chinook Salmon Spawning

Fall-run Chinook Spawning Requirements

Chinook dig a redd (nest) and deposit their eggs within the stream sediment where incubation, hatching, and subsequent emergence take place. Spawning typically occurs in gravel beds that are often located at the tails of the holding pools (USFWS 1995, CDFG 1998b). Chinook salmon generally spawn in water from one to three feet deep, however, spawning can occur in depths from 0.5 to greater than 20 feet deep (CDFG 1998b). Other criteria include water velocities of 1 to 3.5 feet per second, a gradient of 0.2 to 1.0 percent, substrate from 0.5 to 10 inches dominated by 1- to 3-inch cobble, and escape cover (CDFG 1998b; Puckett and Hinton 1974). The upper preferred water temperature for spawning adult Chinook salmon has been identified as 55°F (Chambers 1956) to 57°F (Reiser and Bjornn 1979) which is similar to the upper preferred water temperature for migration (56°F)

Existing Stanislaus River Conditions and Effects on Fall-run Chinook Spawning

Based on several spawning surveys and environmental studies, there appear to be several factors that may influence fall-run Chinook spawning and spawning habitat in the Stanislaus River including limited spawning gravel supplies; substrate armoring and embeddedness; and increased turbidity levels. Spawning habitat has been altered as a result of reduced gravel recruitment due to gravel mining and blockage of coarse sediments and reduced sediment transport flows caused by dams, and changes in streamside land use.

Natural riverine habitats are created and maintained by geomorphic and hydrologic processes that result from the interactions between flowing water and sediment supply, and from the secondary influences of large woody debris (McBain and Trush 2003). It is the structure, complexity, and connectivity of these habitats combined with other factors, such as land use and species introduction, which regulate species abundance and distribution. These processes have

21

michele simpson, 01/06/04,

Primarily during fishing season? Or at other times too?


been substantially altered in the Stanislaus River by anthropogenic activities such as gravel and gold mining; removal of large woody debris; agricultural and urban development; land, water, hydroelectric, and flood control project development. The Stanislaus River is considered to have the most degraded channel complexity of the San Joaquin tributaries (CALFED 1999).

Instream gravel and gold mining peaked during the early 1940s (Frymire, personal communication, 2000) and ceased sometime prior to 1980 (exact dates are unknown because gravel miners are not required to maintain records). During this time, approximately 40% of the spawning habitat was excavated from the 11.4-mile reach between Goodwin Dam (RM 58.3) and the Orange Blossom Bridge (RM 46.9; Appendix 2) which is where most Chinook salmon currently spawn in the lower Stanislaus River (Figure 1). There are only a few sections of the river between Knights Ferry (RM 54) and the Orange Blossom Bridge that were not mined. The riffles in the unmined areas were usually well used by spawning salmon in fall 1994 and 1995 compared to the riffles that remain in the mined reaches. One possible explanation is that although riparian encroachment since the construction of New Melones Reservoir in 1979 and pre-1970 dike construction have accelerated the scour of gravel from spawning riffles, gravel that is scoured from the riffles in the unmined reaches provides recruitment for the downstream riffles. Over time, the upstream most riffles in the unmined reaches typically became degraded whereas the downstream riffles usually contain abundant gravel and still function as high quality spawning and rearing habitat. Furthermore, there is a small amount of remaining floodplain habitat in these reaches that probably helps remove fines from the active channel and minimize the rate of scour. Conversely, the riffles in the mined reaches are typically isolated between ditches or ponds, and so the gravel is scoured away during high flows due to the absence of gravel recruitment.

Flow regulation, combined with direct habitat degradation by dredging and instream mining activities, have disrupted the geomorphic and hydrologic processes responsible for creating and maintaining natural riverine habitats downstream. Upstream dams have blocked nearly the entire coarse sediment supply to the lower river (Kondolf and others 2001). The limited amount of coarse sediments entering the river from areas below Goodwin Dam are often captured in the dredged channels and instream mine pits that exists in the lower river which further limits gravel recruitment to areas downstream from these dredged areas. As a result of decreased coarse sediment supplies due to the dams and to the capture of sediments by dredged areas, the lower river channel has become narrower and deeper in some areas while wider and shallower in others (Kondolf and others 2001) and many of the gravel beds have become armored (i.e., consist of large gravel, cobbles, and boulders that are too heavy for the current to move) and smaller as the gravel has gradually eroded away.

Additionally, the management of the upstream reservoirs has reduced the frequency of high flows downstream from Goodwin Dam. In natural riverine ecosystems, flooding increases the rate that gravel is scoured from riffles while fines are deposited on the floodplain and relatively clean gravel is deposited on the riffles during the descending limb of the hydrograph (Kondolf and others 2001; McBain and Trush 2003). If this process is impaired and fines fill the interstitial spaces in the gravel beds, the bed becomes more resistant to mobilization during high flows and the habitat can become unsuitable for both invertebrates and incubating salmonid eggs (McBain and Trush 2003).

Since New Melones Reservoir was constructed in 1979, flows between 5,000 and 8,000 cfs,

22


which could mobilize the streambed, have occurred only during spring 1983 and 1997; prior to 1979, these flows occurred every 1.5 to 1.8 years on average (Kondolf and others 2001). Moreover, flows substantially higher than 8,000 cfs that would cause channel meander and avulsion (i.e., sudden and perceptible loss or addition to land by the action of water, or a sudden change in the bed or course of a stream) and prevent riparian vegetation encroachment in the active channel (Kondolf and others 2001) has not occurred since January 1969 when a maximum daily flow of 16,200 cfs occurred. As a consequence, riparian vegetation has rapidly encroached on the exposed gravel bars and channel meander and avulsion have been substantially reduced (Kondolf and others 2001).

The encroachment of riparian vegetation onto the floodplains has probably increased the rate that gravel is scoured from the riffles and reduced the rate of gravel recruitment (Kondolf and others 2001; McBain and Trush 2003). The vegetation’s root systems tend to bind the gravel in the floodplain, thereby reducing the rate that gravel is recruited to the active river during high flows. Encroachment also tends to confine the flows within the active channel which increases the velocity in the channel and shear stress (force per unit area) on the bed, and thus increases the rate that gravel is mobilized in the active channel. This problem is aggravated when gravel is deposited at the edges of the floodplain where the encroached vegetation reduces the water velocities over the floodplain; this situation has occurred just downstream of the Knights Ferry County Bridge. Together these two effects have accelerated the rate of channel incision and channel widening in the Stanislaus River (Kondolf and others 2003).

The high concentrations of fines and cemented gravels in the spawning beds in the Stanislaus River (DWR 1994; Mesick 2001a; CMC 2001) is probably due to the combined impacts of (1) infrequent bed mobilization (McBain and Trush 2003), (2) fines that are stored in dredged areas and then mobilized during annual pulse flows (CMC 2002a), and (3) the loss of functional floodplain habitat (Kondolf and others 2001; McBain and Trush 2003). CMC (2002a) reported that bed permeability significantly declined in spawning beds that had been recently constructed in or near dredged channels immediately after relatively clear flood control releases of 1,500 cfs began in February 2000. Both the ditch-like dredged channels and captured mine pits contain large volumes of fines that are mobilized during flows of about 1,500 cfs or more. Even during the high spring flows in spring 1997, which peaked at 7,350 cfs, newly deposited gravel in spawning beds contained high concentrations of fines (Mesick 2001a) It is likely that high flows do not flush fines from the streambed onto the floodplain in the Stanislaus River because extensive riparian encroachment and dikes minimize the flow of silt-laden water over the floodplain in the Stanislaus River.

Fall-run Chinook Spawning Habitat Distribution. The historic spawning reach for fall-run Chinook salmon has been described as a ten-mile reach that extended from the marshlands above Oakdale (possibly Kerr Park) to Knights Ferry by Clark (1929). Today, Chinook spawning typically occurs between Goodwin Dam and Jacob Meyers Park in Riverbank at about 120 natural riffles. Between 1994 and 1996, redd density only slightly declined in a downstream direction (Figure 9; CMC 2001; Mesick 2001a), however, in fall 1998, redd densities declined substantially in a downstream direction (Figure 9; CMC 2001, 2002a, and 2002b). It does not appear that spawners necessarily used the downstream areas less in 1998, but rather, as the number of spawners increased three-fold from 1,031 in 1994 to 3,147 in 1998, a majority of spawners made use of the riffles above Oakdale, while use of the spawning grounds below Oakdale remained minimal.

23


Fall-run Chinook Preferred Spawning Areas. Fall-run Chinook spawing surveys in 1994 and 1995 indicated that approximately 73% of redds occurred in the uppermost 30-foot sections of spawning riffles even though habitat in the downstream sections of these riffles appeared to have similar water depths, velocities, and gravel sizes compared to the highly used upstream sections (Mesick 2001a). Detailed measurements at 12 riffles indicated that most redds were constructed where the streambed was rising in a downstream direction (e.g., tail of a pool); intragravel DO concentrations were usually high at these areas although downwelling could not be detected with a water-filled manometer (Mesick 2001a). This apparent preference for spawning at the tail of pools is commonly observed for fall-run Chinook in other watersheds as well (USFWS 1995, CDFG 1998a).

0.05

0.1

0.15

0.2

0.25

Red

ds P

er S

quar

e-Ya

rd

0 5 10 15 20 25Miles Below Goodwin Dam

1994 1995 1996 1998

Stanislaus River Redd Density

Figure 9. Fall-run Chinook salmon redd density relative to the distance below Goodwin Dam in fall 1994, 1995, 1996, and 1998. The regressions for these relationships are shown as the four lines.

Due to the observed preference of salmon for the uppermost sections of riffle areas, redd superimposition (i.e., a new redd is built over a pre-existing redd) may be a substantial problem for salmon in the Stanislaus River. High rates of redd superimposition have been observed in the Stanislaus River since 1994 regardless of the number of spawners. It appears that most spawning adults prefer to spawn in a relatively few upstream sites where much of the spawning habitat was previously excavated.

Armoring and Embeddedness and Fall-run Chinook Salmon Spawning. Approximately 40% of salmon spawning habitat has been mined for gravel and 33% of the riffles between Goodwin Dam and the Orange Blossom Bridge have become somewhat armored due to the lack of gravel

24


recruitment resulting from gravel mining, as well as blockage of sediments and reduced sediment transport flows caused by the dams (Appendix 2). It is possible that this reduction in the availability of spawning habitat has increased the rate of redd superimposition. Gravel has been added to several sites in Goodwin Canyon since 1997 by CDFG and to 18 sites between Two-Mile Bar and Oakdale in 1998 (CMC 2002a) to restore gravels lost. However, the amount of gravel that has been added to the river is less than 1% of the estimated 1,031,800 cubic-yards of gravel that was excavated from the active channel between 1939 and 1999 as evidenced by aerial photographs (Kondolf and others 2001). It is believed that in-channel mining ceased sometime during the 1960’s, so most if not all of the excavation took place prior to that time.

Most of the riffles that were left undisturbed in the mined areas are now either somewhat armored, such that large rocks which are difficult for the adults to move, cover the surface layer of the streambed, or they are embedded with sediment, especially sand, which packs tightly (embeds) into spaces between stones and gravels in the river bed. As a result, it is likely that adult salmon tend to create new redds on top of existing redds in the Stanislaus River simply because it is easier to dig a new redd in areas where existing redds have been constructed compared to nearby areas that are covered with large rocks or highly embedded. Redd superimposition is likely to have the greatest impact on redds constructed early in the season (e.g., late October and early November) because they would be the most vulnerable to late-arriving fish. Based on fall 2000 studies with artificial redds (CMC 2002b), approximately 33% of early redds were completely destroyed during redd superimposition and another 21% of the early redds were buried by fines re-suspended during later redd construction and deposited on existing redds. This likely entombed many of the alevins and reduced the downwelling of oxygen-rich surface water into the egg pocket. These percentages may be similar in other years but are likely influenced by spawner density. Mortality rates due to entombment in superimposed and silted redds have not been quantified.

Turbidity and Fall-run Chinook Spawning. Another potential problem for spawning fish is increased turbidity and siltation from storm run-off as a result of changes in land use, such as new housing developments. For example, following an intensive rainstorm in late January 2000, a thick blanket of clay-sized silt covered the riffles at Knights Ferry and downstream areas, particularly those below the Orange Blossom Bridge (CMC 2002a). Since this amount of silt had not been observed following intensive storms in January 1996, it is possible that changes in land use since that time, namely increased housing development, could be responsible.

Agriculture in the upper spawning reach, which consists primarily of grazing, is also likely to contribute to increased turbidity from the erosion of unpaved roads and the trenching of pastures to drain standing water that accumulates during intensive rainstorms. However, bank erosion only occurs at isolated locations and does not appear to be a substantial problem between Goodwin Dam and Oakdale.

2.1.5 Fall-run Chinook Salmon Incubation and Emergence

Fall-run Chinook Incubation and Emergence Requirements

Optimum substrate for embryos is a gravel/cobble mixture with a mean diameter of one to four inches and a composition including less than 5% fines (particles <0.3 inches in diameter; Platts and others 1979; Reiser and Bjornn 1979; CDFG 1998b; McEwan and Jackson 1996). In order to

25


keep eggs well oxygenated while they incubate in redds, gravels must be free of silt and fine sediments to allow the permeation of flowing water. Eggs incubating in clean laboratory conditions can survive at DO concentrations as low as about 2 mg/l whereas those incubated in silty, natural environments require up to 8 mg/l DO concentrations for survival (CMC 2002a). Studies have shown that redd building activity itself generally cleans the redds of fines <1 mm down to about 7%, however, when silts are mobilized again, they can quickly re-infiltrate clean gravels (CDFG 2002b).

Egg survival rates are also highly dependent on water temperature. The optimum temperature range for Chinook salmon egg incubation according to Rich (1997) is 44°F to 54°F1. However, Chinook salmon eggs had highest survival in the American River when water temperatures were 53°F to 54°F (Hinze and others 1959; Boles and others 1988) while survival of Chinook salmon eggs and larvae during incubation declined as water temperatures increased to 53.6–60.8ºF (Myrick and Cech 2001). Incubating eggs from the Sacramento River showed reduced viability and increased mortality at temperatures >58°F, and suffered 100% mortality at temperatures >65° F (Seymour 1956; Boles and others 1988) and ≤35°F (Velson 1987; CDFG 1998c). The time for incubating eggs to reach specific embryonic developmental stages is determined by water temperature; increased temperatures within non-lethal limits decrease emergence times. For example, at an incubation temperature of 56°F (13°C), eggs would be in the gravel approximately 70 days.

Existing Stanislaus River Conditions and Effects on Fall-run Chinook Incubation and Emergence

Incubation habitat is affected indirectly by changes in streamside land use. Based on several environmental studies identified below, the primary factor that may influence fall-run Chinook egg incubation and incubation habitat in the Stanislaus River is high concentrations of fines within spawning gravels that result in low DO levels. Also, streamflow may be an influencing factor. On the other hand, water temperatures appear to be suitable for fall-run Chinook incubation.

Fines and Dissolved Oxygen and Fall-run Chinook Incubation and Emergence. Several studies have indicated that there are relatively high concentrations of fines (sand and silt) in the spawning riffles in the Stanislaus River (DWR 1994; Mesick 2001a; CMC 2001). However, Chinook salmon are able to effectively remove most fines during the construction of their redds (CMC 2002b) so high levels of fines are only problematic under certain conditions. Whenever a new redd is constructed, fines are re-suspended and can pose a problem to pre-existing redds located downstream of the new redd by settling out in, and covering the pre-existing redd. This deposition of fines on pre-existing redds can entomb incubating eggs or alevins (CMC 2002b) and sometimes reduce downwelling of oxygen-rich surface flows into the egg pocket.

Turbid storm runoff in January and February can impact incubating eggs located in redds constructed after mid-November. Suspended clay-sized particles in turbid storm runoff can 1 Note: temperature requirements given for all lifestages of Chinook salmon are based on studies conducted outside of the San Joaquin Basin and are often conducted within laboratory conditions using hatchery fish, so “wild” salmon within the San Joaquin Basin may have slightly higher temperature preferences and/or tolerances than those used within this report. Higher temperature preferences and/or tolerances may be due to adaptation of San Joaquin salmon to naturally higher temperature conditions existing at the southernmost extent of their range and/or due to distinctive differences between “wild” and hatchery fish.

26


become deposited in existing redds and penetrate the egg pockets and coat the surface of the eggs. Eggs that are coated with silt have a reduced ability to absorb oxygen (CMC 2002a).

Another problem with turbid storm runoff is that fine sediment intrusion can seal the sand layer covering the egg pocket thereby reducing the downwelling of oxygen-rich surface water flowing into the egg pocket which subsequently increases the percentage of oxygen-poor groundwater circulating into the egg pocket. In February 1996, intragravel DO concentrations declined by 25% to 75% in several artificial redds after four intensive rainstorms in January increased the mean daily flows by an average of 200 to 500 cfs for several days after each storm (Mesick 2001a). Turbidity was not measured during this time.

As a result of the reduced ability to absorb oxygen and/or low oxygen conditions, eggs will either experience mortality or tend to produce stunted alevins. In the case where the sand layer has become sealed, these stunted alevins may be too weak to emerge through the sand layers covering the egg pocket (CMC 2002a); alevins of Chinook salmon and steelhead have been observed in laboratory studies to have difficulty emerging when gravels exceeded 30–40% fine sediments (Bjornn 1968; Phillips and others 1975; Bjornn and Reiser 1991; Waters 1995). In addition, stunted alevins may have difficulty competing with healthy alevins for food after emergence (CMC 2002a). Although low oxygen conditions may affect eggs and the alevins they subsequently produce, those alevins already hatched prior to low oxygen conditions would probably survive low DO concentrations due to their ability to extract as much available DO as possible through their gills.

Streamflow and Fall-run Chinook Incubation and Emergence. Extremely high or low flow fluctuations each have the potential to destroy incubating eggs and/or injure recently emerged alevins. High streamflow events may cause adverse effects by scouring redds or sweeping recently emerged fry downstream, while rapid flow reductions can result in dewatering of redds previously constructed near stream margins. Scouring flows are unlikely to occur in the Stanislaus River due to flood control operations which limit the occurrence of flows in excess of 1,500 cfs. Critical flow reductions that can cause redd dewatering have not been identified at this time since there is no detailed habitat information available for calculating how spawning habitat quantity changes with flow.

Water Temperature and Fall-run Chinook Incubation and Emergence. Thermograph data collected since 1998 during the fall-run Chinook incubation and emergence period indicates that maximum average daily water temperatures did not exceed 60°F in the spawning reach of the Stanislaus River (Figure 7) which is well below absolute lethal (100% mortality) temperatures of 65°F. Although temperatures measured at Knight’s Ferry and OBB were higher than preferred during late October through November, the remainder of the incubation period was within preferred temperatures. In addition, surface and intragravel water temperatures were almost always less than 56°F during late-October and early-November in 1996 (CMC 1997), 1999, and 2000 (CMC 2002a, 2002b) between Goodwin Dam and the Orange Blossom Bridge.

2.1.6 Fall-run Chinook Salmon Juvenile Rearing

Fall-run Chinook Juvenile Rearing Requirements

27


Juvenile rearing habitat must provide adequate space, cover, and food supply (CDFG 1998c). Optimal upstream habitat includes abundant instream and overhead cover (for example, shallow riffles, undercut banks, submergent and emergent vegetation, logs, roots, other woody debris, and dense overhead vegetation) to provide refuge from predators, and a sustained, abundant supply of invertebrate and larval fish prey.

Immediately after emergence, Chinook fry are found in quiet water areas, along the stream bank, close to cover such as tree roots or logs. Fry tend to use low velocity areas where substrate irregularities and other habitat features create velocity refuges and they may increasingly rely on turbidity as cover (Gregory and Levings 1998). As they grow larger, juvenile Chinook move into locations of higher velocity, either along the stream margin or in gravel and cobble interstices further from shore.

Use of floodplain habitat by juvenile Chinook salmon has been well documented (DWR 1999; Sommer and others 2001a and b). Sommer and others (2001b) found that floodplain habitat in the Yolo bypass provided better rearing and migration habitat for juvenile salmon than the main Sacramento River channel. Chinook salmon growth rates in the Yolo bypass were generally higher than growth rates in the main channel. These faster growth rates may be attributed to increased prey consumption associated with greater availability of drift invertebrates and warmer water temperatures.

High water temperatures are generally a concern for juvenile fish in the Central Valley primarily in May and June when water temperatures often exceed optimal rearing temperatures (Myrick and Cech 2001); whereas, low water temperatures in the lower Stanislaus River in December and January should be well tolerated by juvenile Chinook salmon which can tolerate low temperatures near 32°F (Brett 1952; Figure 10). Assessing temperature tolerances of Chinook salmon is complex because many environmental conditions, such as food availability, DO concentration, acclimation temperature, contaminants, and disease can affect their tolerance levels (Myrick and Cech 2001). Under laboratory conditions with well oxygenated, contaminant free water, the chronically lethal temperature for juvenile Central Valley Chinook salmon is 78.8°F (Hanson 1991) and they can tolerate temperatures up to 83.4°F for short periods of time (Myrick and Cech 2001). However, temperature tolerances are not as high under natural conditions. The chronic lethal temperature for juvenile Feather River fish that were marked with coded-wire-tags, released at Ryde in the Sacramento River, and then recaptured in the Delta at Chipps Island between 1983 and 1990 was 73.4°F (Baker and others 1995). Similarly, the chronic lethal temperature for juvenile Chinook salmon held in water pumped from the surface of the American River was 75.2°F (Rich 1987). Although Myrick and Cech (2001) speculated that the relatively low temperature tolerances observed under natural conditions may have been caused by near-lethal water chemistry/quality and/or disease, they did not present data that could be used to verify or quantify these effects.

The optimum temperature range for rearing Chinook salmon fry is 50°F to 55°F (Boles and others 1988, Rich 1997, Seymour 1956) and for fingerlings is 55°F to 60°F (Rich 1997)1. 1 Note: all temperature requirements given are based on studies conducted outside of the San Joaquin Basin and are often conducted under laboratory conditions using hatchery fish. “Wild” salmon in the San Joaquin Basin may have slightly higher temperature preferences and/or tolerances than those cited. Higher temperature preferences and/or tolerances may be due to adaptation of San Joaquin salmon to naturally higher temperature conditions existing at the southernmost extent of their range and/or due to distinctive differences between “wild” and hatchery fish (CALFED 1999).

28


Juvenile Chinook salmon will grow at water temperatures ranging from 46.4°F to 77°F (Brett and others 1982; Clarke and Shelbourn 1985) with optimum growth rates occurring at about 66.2°F for fish fed at maximal rations (Myrick and Cech 2001). However, there are sub-lethal temperature effects that occur below 77°F that include reduced growth rates, impaired smoltification, and increased susceptibility to disease and predation. Fish exposed to low DO concentrations and pathogens may require even lower water temperatures for optimal growth rates (Myrick and Cech 2001). For example, Rich (1987), who reared juvenile salmon in surface water collected from the American River, determined that optimal growth rates for American River fish occurred at 59.5°F. It is also likely that the optimal temperature for growth is further reduced when food rations are low (Brett and others 1969). Based on a model developed for sockeye salmon (O. nerka), Brett and others (1982) determined that temperatures between 66.0°F and 68.9°F produced optimal growth for fish fed at the maximum ration, but that temperatures of about 59°F produced optimal growth for fish fed at 60% of the maximum food ration.

The infectivity and mortality of juvenile salmon from pathogens generally increases as water temperatures increase above 53.6°F based on studies primarily conducted in Oregon and Washington (summarized in Myrick and Cech 2001). There are also sub-lethal effects of elevated water temperatures and pathogen infections that in turn result in reduced growth rates and increased vulnerability to predation (summarized in Myrick and Cech 2001). Marine (1997) reported that predation rates of juvenile fall-run Sacramento River fish by striped bass (Morone saxatilis) increased from about 8% to about 11% when water temperatures increased from a range of 55.4 to 60.8°F to a range of 62.6 to 68°F.

Optimal DO concentrations for salmonids are above 5 mg/L, but salmonids can usually tolerate low DO concentrations (1-2 mg/L) at low temperatures and concentrations close to saturation are required for normal growth and activity (Moyle 2002). However, mortality may result from the combined effects of reduced DO concentrations and other stressors including high water temperatures, disease, contaminants, and predation (Myrick and Cech 2001).

Existing Stanislaus River Conditions and Effects on Fall-run Chinook Juvenile Rearing

The altered geomorphic and hydrologic processes in the lower Stanislaus River probably both degrade and improve juvenile habitat. On the one hand, the dams that have greatly reduced gravel recruitment and controlled flows that allow riparian encroachment on the floodplains and reduce bed mobilization are causing (1) the riffles used by parr-sized juveniles to gradually erode away; (2) a reduction in food availability as the riverbed becomes embedded with fines and the inundation of food-rich floodplains becomes less frequent; and (3) a substantial reduction in the recruitment of Fremont cottonwoods and other large riparian tree species that help sustain channel complexity (Kondolf and others 2001; McBain and Trush 2003).

On the other hand, there may be benefits for juvenile salmonids that result from riparian encroachment. It is likely that riparian encroachment helps to:

1) increase contribution of large woody debris into the river that provides cover and enhances channel complexity. Fremont cottonwoods growing along the riverbank are able to mature along both banks of the lower Stanislaus River due to the controlled flows. The mature trees fall at a high rate into the active channel of the Stanislaus River in spite

29


of the lack of channel migration. However, this benefit may be short-term due to the limited recruitment;

2) increase input of organic matter into the river that drives the food chain. Organic matter accumulates in much higher concentrations in the Stanislaus River than on the floodplains of rivers that have a natural flood frequency;

3) increase overhanging vegetation that provides cover for juvenile salmonids; and 4) increase shading that may help maintain suitable water temperatures for salmonids.

Fluvial geomorphologists generally assume that the impacts resulting from reduced frequency of flooding far outweigh the above potential benefits of riparian encroachment for salmonids (McBain and Trush 2003). One restoration strategy would be to restore key fluvial geomorphic processes while maintaining the benefits provided by riparian encroachment.

Based on fishery studies discussed below, the altered geomorphic and hydrologic conditions have potentially caused changes in density independent factors such as streamflow, turbidity, and contaminants and density dependent factors such as food availability, rate of predation on juvenile Chinook through changes in fish community composition (i.e., more predator habitat results in overabundance of predators), changes in the space available for rearing, and the potential for increased incidence of disease which may influence rearing juvenile fall-run Chinook.

Fall-run Chinook Juvenile Rearing Distribution. Bi-weekly snorkel surveys conducted in 2000 and 2001 indicated that juvenile densities were highest in areas where gravel beds were reconstructed during the summer of 1999 as part of the Knights Ferry Gravel Replenishment Project (KFGRP; Fisheries Foundation 2002). Although no pre-project fish density data exists for comparison, it is presumed that the newly constructed gravel beds provided: (1) improved DO concentrations, (2) reduced predator populations, (3) refuge from predators, and (4) increased food availability which attracted juvenile Chinook. However, these benefits have not been quantified and the attraction of juvenile salmon to these restoration sites is not an indication of improved juvenile survival.

Soon after emergence between mid-December and mid-February, concentrations of fry were observed in slow-water, margin habitats of eight study sites from about a mile below Goodwin Dam downstream to Oakdale in 2000 and 2001 (Fisheries Foundation 2002). Fry densities were highest between Knights Ferry and Honolulu Bar, which is the same reach where most spawning occurred. As fish grew larger through the spring, juvenile salmon became evenly distributed between Two-Mile Bar and Oakdale, where they were found to be relatively abundant in fast-water, riffle habitat, particularly at the KFGRP restoration sites. Due to poor visibility, the Fishery Foundation surveys did not address Chinook distribution, nor the suitability of habitat for rearing juveniles below Oakdale. Although juvenile salmon utilized fast-water areas without bankside vegetation, densities were highest where bankside vegetation provided cover adjacent to fast-water habitat.

During the summer months through mid-September, large juveniles continued to be observed downstream to the Orange Blossom Bridge site. From September 27 to November 19, 2001, few juveniles were observed in the river indicating most had emigrated prior to this time, and only a few remained to emigrate as yearlings.

30


Streamflow and Fall-run Chinook Juvenile Rearing. Existing minimum fishery flows in the lower Stanislaus River were designated in a 1987 study agreement between USBR and CDFG. This agreement, enacted under a CDFG protest of USBR’s water right applications to redivert water from New Melones Dam, specifies interim annual flow allocations for fisheries between 98,300 AF and 302,100 AF depending primarily on carryover storage at New Melones and inflow. The CDFG has the authority to shape this volume of water at their discretion.

Fishery flow targets recommended by CDFG (1993) for the lower Stanislaus River were formulated for salmon spawning, egg incubation, and rearing from October through March and for smolt outmigration during April and May based on results of an instream flow study (Aceituno 1993) and CDFG smolt survival studies, respectively. Spring flows are consistent with meeting spring outflow objectives proposed for the San Joaquin River basin at Vernalis under the Vernalis Adaptive Management Plan. Summer flows are adjusted on a real-time basis to meet water quality standards at Orange Blossom Bridge, Ripon and in the Delta, all of which address needs of oversummering yearling salmon and steelhead in the Stanislaus River.

Water Temperature and Fall-run Chinook Juvenile Rearing. Adherence to water quality standards for temperature and dissolved oxygen within the Stanislaus River and Delta ensure that water temperatures in the Stanislaus River are maintained within a suitable range for juvenile fall-run rearing (Figure 10). On average, maximum daily water temperatures are between 50o F and 60o F from January through May.

Figure 10. Average maximum daily water temperatures and juvenile Chinook rearing requirements at Caswell, Oakdale, and Knight’s Ferry, 1998-2003. Preferred range encompasses fry (50°F to 55°F; Boles and others 1988; Rich 1997; Seymour 1956) and fingerlings (55°F to 60°F; Rich 1997); chronic stress threshold (CDFG 2002a); lethal limit (Baker and others 1995).

40

50

60

70

80

Te

mp

era

ture

(F

)

01-Jan03-Feb

07-Mar09-Apr

12-May14-Jun

17-Jul19-Aug

21-Sep24-Oct

26-Nov29-Dec


Average Maximum Daily TemperatureAnd Juvenile Chinook Requirements

LethalLimit

PreferredRange

ChronicStress Threshold

31


Temperature data collected during outmigration studies from 1999-2003 (SPC unpublished data) indicate that maximum average daily February and early March water temperatures at Caswell were similar between above-normal water year types (1999-2000) when fry survival was high and dry water year types (2001-2003) when fry survival was low (Figure 11), so temperature does not appear to be a factor in fry survival. However, it is possible that an increase of approximately five degrees in water temperature during portions of March, April, and May in 2001-2003 may have reduced the survival of parr and smolt-sized fish compared to the conditions in 1998-2000 (Figure 11 and Figure 18). Maximum daily water temperatures between 60°F and 65°F in March, April, and May of 2001 and 2002 may have resulted in poor growth and condition of juveniles in the lower Stanislaus River, particularly if DO concentrations, food availability, and/or habitat suitability were inadequate in the lower river. If juveniles were in poor condition in 2001-2003, they may not have been able to smolt, avoid predators, or resist disease as well as the fish in 1998-2000.

40

50

60

70

Tem

pera

ture

(F)

01-Jan16-Jan

31-Jan15-Feb

01-Mar16-Mar

31-Mar15-Apr

30-Apr15-May

30-May

Dry Years (2001-2003)Wet Years (1998-2001)

Maximum Average Temperature at Caswell

Figure 11. Maximum mean daily water temperature at Caswell State Park in the lower Stanislaus River during above-normal water years (1998, 1999, and 2000,), and dry water years (2001, 2002, and 2003).

Dissolved Oxygen and Fall-run Chinook Juvenile Rearing. Since 1999, DO has been consistently measured at Ripon which has encompassed a range of water year types from dry to wet years with corresponding low to high flows. The minimum average daily DO (i.e., the lowest average DO value recorded on a particular date for the period of record) at Ripon has generally ranged from 7 to 10, and only fell below 5 mg/L on one day during the four years of monitoring (Figure 6) indicating that DO in the Stanislaus River is not likely to be a problem for juveniles.

32


However, DO has not been consistently measured in the large in-river gravel mine pits. These previously mined areas collect decaying organic matter and provide virtually no flow turbulence such that DO concentrations could be reduced within and downstream of these mine pits. DO in these mine pits would probably be lowest at night when aquatic plants stop photosynthesizing and during late spring when water temperatures become relatively high. A decline in DO at the Oakdale Recreation Pond was observed during two surveys in November 1995 when water temperatures averaged 53.6°F. During these surveys, the mean daytime DO concentration of the surface flow upstream of the Oakdale Recreation Pond at RM 42.4 was 11.0 mg/L, whereas it was 9.5 mg/L within the pond at RM 39.4 (CMC and others 1996). On the other hand, no decline in daytime DO concentration was observed as water flowed from a high gradient section near RM 53.5 through a long ditch-like channel with two small mine pits near Frymire Ranch at RM 52.8 from 1998 to 2000 (CMC 2002a, 2002b). These were wet and average flow years, and no monitoring was conducted during recent dry years. Nighttime DO concentrations have not been measured at the Oakdale Recreation Pond, nor at smaller pits (e.g., Willms Pond) or in the dredged ditch-like channels.

Predation and Fall-run Chinook Juvenile Rearing. Studies conducted in the Stanislaus River by the SPC, CDFG, and the Fisheries Foundation suggest that predation may substantially affect juvenile outmigrant survival under certain conditions, such as low flows and/or high water temperatures. Studies conducted outside of the San Joaquin basin suggest that predation of juvenile salmonids primarily occurs where flows are altered and predators are abnormally abundant, and, that under natural riverine conditions, salmonids are not major prey items of species such as pikeminnow (Brown and Moyle 1981). Other studies also suggest that habitat types can affect whether predators feed on juvenile salmonids. For example, Zimmerman (1999) reported that juvenile salmonid predation was much greater for northern pikeminnow than for smallmouth bass and walleyes (Stizostedion vitreum) through the lower unimpounded Columbia River, but not in the John Day Reservoir.

SPC Radio Tracking Studies. Radio tracking studies conducted by S.P. Cramer & Associates during May and June of 1998 and 1999 (Demko and others 1998; SPC unpublished data) suggest that the survival of large naturally produced and hatchery juveniles, 105 to 150 mm fork length, was less than 10% in the Stanislaus River downstream of the Orange Blossom Bridge (Demko and others 1998). Radio tagged fish (gastrically implanted transmitters with 12-inch external whip antennas) ceased to migrate most frequently at four different sites on the Stanislaus River during both years (; SPC unpublished data):

1) A large pond below the Orange Blossom Bridge at RM 46.3 2) Near the Oakdale Recreation Pond at RM 39.753) Near McHenry Park at RM 28.54) Near Ripon at RM 16.0

33


0

5

10

15

# of

Tag

s

0 3 6 9 12 15 18 21 24 27 30 33 36 39 42 45 48River Mile

Lowest River Mile Achieved

Reach 3 Reach 2 Reach 1

Figure 12. The lowest river mile achieved by radio-tagged smolts in 1999.

SPC (unpublished data) electrofishing surveys conducted in the main channel and ponds at the Oakdale and McHenry recreation areas during May and June 1999 indicate that several predatory species were present (Table 1). Largemouth bass and small Sacramento pikeminnow were found primarily in the backwater/pond habitats (Figure 13). In contrast, a majority of the juvenile Chinook salmon and striped bass were found in the main channel (Figure 13). No large pikeminnow were observed. Gastric lavage revealed that two of the striped bass collected just upstream of the Oakdale Recreation Area Pond and one near McHenry Park had ingested radio tagged salmon. None of the largemouth bass or pikeminnow collected had juvenile salmon in their stomachs.Table 1. The number and size of fish collected during electrofishing surveys in captured mine ponds at the Oakdale Recreational Park and McHenry Park and in the river’s main channel 1-2 miles upstream and downstream of the Oakdale Recreation Pond in May and June 1999 (SPC, unpublished data).

Species MAY JUNECommon Name Family N AVG STD MAX MIN N AVG STD MIN MAX

Black Bullhead Ictaluridae 1 229 0Chinook Salmonidae 16 74 8 92 60 0

O. mykiss Salmonidae 2 284 37 310 258 0Striped Bass Percichthyidae 1 815 8 405 126 285 688

Brown Bullhead Ictaluridae 2 216 15 226 205 3 171 16 160 189Tule Perch Embiotocidae 5 129 22 164 104 0

Carp Cyprinidae 34 478 58 609 390 2 398 18 385 410Goldfish Cyprinidae 2 255 100 325 184 0

Hitch Cyprinidae 4 151 33 191 115 0Sacramento Blackfish Cyprinidae 8 366 54 428 276 2 416 48 382 450

Sacramento Pikeminnow Cyprinidae 8 171 36 234 136 2 335 211 186 484Hardhead Cyprinidae 9 406 29 468 378 0

Riffle Sculpin Cottidae 1 95 0Black Crappie Centrarchidae 4 143 65 220 64 4 177 31 131 197

Blue Gill Centrarchidae 2 72 34 96 48 5 127 21 108 157Largemouth Bass Centrarchidae 16 347 95 515 185 8 297 83 202 415

Pumpkinseed Centrarchidae 1 156 0Redear Sunfish Centrarchidae 3 181 29 211 154 3 171 19 157 193

Smallmouth Bass Centrarchidae 1 195 0White Crappie Centrarchidae 1 74 0

Sacramento Sucker Catostomidae 26 386 123 516 133 0

34


The signals from ten tagged fish were tracked in and out of the ponds at the Oakdale Recreational Park and McHenry Park in 1999, some of which moved at speeds greater than 16 feet/second, a speed capable of adult striped bass (Castro-Santos and Haro 2000). Juvenile salmon are only capable of speeds of less than 1 ft/s (Peake and McKinley 1998). Striped Bass were observed during SCUBA and electrofishing surveys in May and June 1999 at Orange Blossom Bridge, the Oakdale Recreation Area, and McHenry Recreation Area where the tagged fish ceased their migrations (SPC, unpublished data).

Although many of the radio-tagged fish appear to have been eaten by predators, there is uncertainty as to whether the tagging procedure affected the fish’s vulnerability to predators. Gastric implantation is stressful to juvenile salmonids and the whip antenna impairs their swimming ability (Vogel, personal communication, X). During the 1998 SPC studies, only 73% of the fish survived the tagging procedure and no evaluations were made to determine whether fish behavior was affected by tagging (Demko and others 1998).

0

0.2

0.4

0.6

0.8

1

% o

f Tot

al fo

r eac

h S

peci

es

Pikeminnow Largemouth Striped bass ChinookSpecies

Main Channel Pond/Backwater

Frequency of Predators and Chinookin Main Channel and Pond

Figure 13. Frequency of predator species and juvenile Chinook salmon in main channel and pond/backwater habitats near the Oakdale Recreation Park and McHenry Park in the lower Stanislaus River in May and June 1999 (SPC, unpublished data).

The observed abundance of largemouth and smallmouth bass in the Stanislaus River during SPC studies in 1998 and 1999 may have been relatively low due to higher water flows and associated low temperatures. Hook-and-line fishing for largemouth and smallmouth bass in the Stanislaus

35

Andrea Fuller, 01/06/04,

When?


River was particularly good during the 1987 to 1992 drought, but became quite poor after the 1995, 1997, and 1998 floods according to numerous local sport anglers and residents. These observations suggest that black bass may be displaced by high flows and low water temperatures. It is possible that their populations could be increasing as a result of the recent dry water year conditions.

The SPC radio-tagging and electrofishing studies, which represent the greatest amount of information regarding predation available within the lower Stanislaus River, were limited to the months of May and June after most juvenile salmon had already emigrated. These studies did not evaluate juvenile salmon movement or species composition between January and early May so uncertainty remains as to whether predation may explain the low screw-trap survival estimates for fry and parr between the Oakdale and Caswell State Park study sites in 2001, 2002, and 2003.

If predation does contribute to substantial mortality of salmon fry and parr in the Stanislaus River downstream of Oakdale, then turbidity is also likely of significant importance. The potential predatory species within the river are visual predators which primarily use their vision to detect and attack prey. High turbidities can impair visual abilities, thus reducing the detection range of predators and allowing small fish to outmigrate undetected. The high turbidity that occurred during high flows in February and March of 1999 and 2000 (Figure 14) could have reduced predation rates which could then explain the relatively high screw trap survival estimates in 1999 and 2000 compared to 2001 and 2002.

0

10

20

30

40

50

Turb

idity

(NTU

)

01-Jan16-Jan

31-Jan15-Feb

01-Mar16-Mar

31-Mar15-Apr

30-Apr15-May

30-May

Dry Years (2001-2003)Wet Years (1998-2000)

Maximum Daily Turbidity at Caswell

Figure 14. Maximum daily turbidity (Nephelometric Turbidity Units) recorded at the screw trap at Caswell State Park in above-normal water years (1998 and 2000), and in dry water years (2001, 2002 and 2003; SPC 2003).

36


CDFG Electrofishing Studies.. The CDFG (undated memorandum) conducted a single-pass electrofishing survey in the Oakdale Recreation Area Pond in the late 1980s. According to the memo, subsequent stomach content analyses suggested that several species of centrarchids were preying on juvenile salmonids. The actual species captured and the survey date are unknown.

Fish Foundation Snorkel Surveys. Other potential predators include the riffle sculpin (Cottus gulosus), adult American shad (Alosa sapidissima), and the Sacramento pikeminnow. Although predation rates of riffle sculpin are unknown, the riffle sculpin is relatively abundant in the Stanislaus River (SPCA 2003) and may prey upon salmon fry since other species of sculpins, such as the prickly sculpin (C. asper) and the torrent sculpin (C. rhotheus), are known to prey on salmonid fry (Patten 1971; Tabor and others 1998). No information was reported by the Fish Foundation regarding their observations of abundance or distribution of Sacramento pikeminnow or riffle sculpin.

Schools of 20 or more American shad were observed in June and July near Lovers Leap (Fisheries Foundation 2002), but were absent during surveys in other months surveyed from March through December 2000 and January through June 2001. Since relatively few shad and juvenile Chinook have been observed residing in the river at the same time, shad predation of salmon juveniles is expected to be low.

Observations Reported by Fishermen. It has been reported by fishermen that some of the striped bass in the Stanislaus River are residents and others are migratory, so at least some individuals are present throughout the juvenile Chinook rearing and migration period. One fishing guide, Michael Swaney, reports that he captured several striped bass in March, and sight-fishes for them throughout most of the year, spotting schools of 10 to 30 fish with some over 40lbs (http://www.fishbernard.com/stanislaus1.html). The same guide states that these fish are in habitat that is not the norm for striped bass.

Another fishing guide, Steve Walser, reports that adult Sacramento pikeminnow have been observed to form large schools in the Stanislaus River between Knights Ferry and the confluence with the San Joaquin River, and prey extensively on salmon fry in January and February (Walser, personal communication, X).

Tuolumne River versus Stanislaus River Predation Studies. In the nearby Tuolumne River, studies indicate that predation of juvenile salmon occurs primarily by largemouth bass (Micropterus salmoides) and smallmouth bass (M. dolomieu) which are both associated with large captured mine pits. In contrast, studies and observations in the Stanislaus River suggest that predation is likely due to Sacramento pikeminnow (Ptychocheilus grandis) and striped bass, both of which primarily inhabit ditch-like channels (a.k.a., “special run-pools” by EA Engineering) that are relatively common downstream of Knights Ferry. One explanation for the difference observed in predator species between rivers is that the Tuolumne River and Stanislaus River studies were conducted under different flow conditions which may support different predator species. Studies on the Tuolumne River were conducted during the 1987-1992 drought when flows were low, whereas, the Stanislaus River studies were primarily conducted after a series of floods in 1998 and 1999 when flows were high. The low flows on the Tuolumne River likely provided better habitat conditions for largemouth and smallmouth bass which are more suited to low flows and high water temperatures, while, the higher flows on the Stanislaus River provided

37


When?


Sacramento pikeminnow and striped bass better conditions since they can function well over a wide range of flows and water temperatures.

Another explanation for the difference observed in predator species is that Tuolumne River and Stanislaus River studies examined juveniles of different origins which may have different rates of susceptibility to different predators. In the Tuolumne River, a large number of hatchery juveniles were released during the predation study, whereas, in the Stanislaus River Chinook were primarily of “natural” origin. The riverwide electrofishing surveys conducted in the Tuolumne River during spring 1989 and 1990 concluded that largemouth and smallmouth bass are substantial predators of juvenile salmon. However, very few bass contained juvenile salmon in their stomachs when only natural origin Chinook were present. In contrast, a much greater proportion of the bass sampled during May 1990 contained juvenile salmon in the stomachs coincident with a release of 93,653 hatchery reared salmon smolts and higher flows at Old La Grange Bridge. This indicates that hatchery origin Chinook may be more susceptible to predation than natural origin Chinook, and that bass predation may only be substantial under certain conditions (Table 2).

Table 2. EA Engineering, Science, and Technology predation studies in the lower Tuolumne River in 1989 and 1990 (EA 1992).

Sampling Dates La Grange Flows (cfs)

% Largemouth Bass with juvenile salmon in their stomachs

% Smallmouth Bass with juvenile salmon in their stomachs

Origin of Juvenile Salmon

4/19 to 5/17, 1989 40 – 121 3.6% (2/56) 8.6% (5/58) Naturally Produced



5/2 to 5/4, 1990 299 -572 26% (40/152) 33.3% (6/18) CWT Hatchery

Although EA Engineering estimated that almost 70% of the tagged hatchery fish died during their three-day migration from the La Grange Bridge to the confluence with the San Joaquin River, presumably from predation, the results of their study may not be straightforwardly applied to the population of naturally produced fish in the Stanislaus River due to differences in fish behavior and testing conditions. First, naturally produced juveniles usually migrate at night when predation rates are lowest, whereas, hatchery fish typically migrate during the day (Roper and Scarnecchia 1996) and are thought to be naïve at avoiding predators which would likely result in higher predation rates observed on the Tuolumne associated with hatchery fish. Second, relatively few bass were observed feeding on naturally produced fish particularly in early 1990 when salmon densities would have been highest and water temperatures were low. This could be interpreted to indicate that the feeding rates of the bass were lower during this time of year due to lower temperatures, and/or that naturally produced fish were less susceptible to predation than hatchery fish. Finally, the Tuolumne River predation study was conducted under flows that are much lower than those typically released in the Stanislaus River and these lower flows may provide better habitat conditions, such as warmer temperatures, for bass predators. Higher flows in the Stanislaus River may reduce water temperatures which would likely result in lower bass predation rates observed on the Stanislaus than on the Tuolumne River.

38


Disease and Fall-run Chinook Juvenile Rearing. The USFWS conducted a survey of the health and physiological condition of juvenile fall-run Chinook salmon in the San Joaquin River and its primary tributaries, the Stanislaus, Tuolumne, and Merced rivers, during spring 2000 and 2001 (Nichols and Foott 2002). Renibacterium salmoninarum, the causative agent of Bacterial Kidney Disease (BKD), was detected in naturally produced juveniles caught in rotary screw traps from the Stanislaus and Tuolumne rivers and juveniles caught with a Kodiak trawl at Mossdale in the San Joaquin River. However, no gross clinical signs of BKD were seen in any of the fish examined. Although no symptoms were observed, these low-level infections can remain active and clinical symptoms may subsequently develop after the fish enters the ocean.

Proliferative kidney disease (PKD) was detected in both natural and hatchery juveniles from the Merced and mainstem San Joaquin rivers in 2000 and 2001 (Nichols and Foott 2002) and in natural juveniles from the Merced River in 2002 (Nichols 2002). The myxozoan parasite Tetracapsula bryosalmonae, which causes PKD, was detected in the kidney samples of only 2% of the juvenile Merced River fish in April 2000, but in 90% of the April 2001 samples, 100% of the May 2001 samples, and 51% of the April 2002 samples. Heavy infections were observed in 22% of the samples in 2002 (Nichols 2002). These data suggest that the incidence of pathogen infection is low in above normal water years such as 2000 compared to dry water years such as 2001 and 2002. PKD has been described at the Merced River Fish Hatchery since the 1980’s and in California since at least 1966. It compromises the fish’s performance in swimming, salt water entry, and disease resistance (Nichols and Foott 2002). Nichols and Foott (2002) suggested that proliferative kidney disease could be a significant contributor to mortality in natural fish. Although none of the fish evaluated from the lower Stanislaus River were infected with this parasite, it is possible that they may become infected when they migrate into the San Joaquin River and Delta, where the infection has been observed (Nichols and Foott 2002).

Pathogenic species of bacteria, such as Aeromonas salmonicida, Yersinia ruckeri and Edwardsiella tarda, were not detected in any of the samples and there were no signs of infection or disease associated with these species (Nichols and Foott 2002). Although Myxobolus cerebralis, the causative agent of whirling disease, was not detected in a pooled sample of 194 Chinook, the parasite has been detected in rainbow trout from the Stanislaus River. Tests were not conducted for Flavobacterium columnare. The disease Ceratomyxa is present in the Central Valley, although it was not detected in studies conducted in the Stanislaus River (Nichols and Foott 2002). Other studies indicate that this disease causes a high mortality rate of Chinook smolts migrating through the lower Willamette River, Oregon (Steve Cramer, personal communication, X). This disease relies on tubifix worms for an intermediate host and the worms flourish in organic sediments. It is likely that the worms multiply and the disease spreads in years when organic sediments are not flushed by high flows. There are indications that mortality of smolts due to this disease increases in drought years and decreases in wet years. This disease is of particular concern for the Stanislaus River because there is a tubifix worm farm near the Orange Blossom Bridge which poses a potential risk. It is also possible that organic sediments accumulate and naturally produce tubifix worms in captured mine pits.

At this time, the potential magnitude of health issues associated with BKD and PKD in the Stanislaus River is unknown. Nichols and Foott (2002) recommended that monitoring the

39


When?


incidence of BKD and PKD in the San Joaquin basin should be continued to determine their impact to the natural fish population.

Contaminants and Fall-run Chinook Juvenile Rearing. Although contaminants in the San Joaquin basin may not have direct effects on fish health, they may have indirect effects. For instance, a study conducted in Puget Sound, Washington, (Arkoosh and others 1998) indicates that emigrating juvenile Chinook salmon exposed to contaminants, polycyclic aromatic hydrocarbons, and polychlorinated biphenyls, suffered increased susceptibility to the common marine pathogen (Vibrio anguillarium). The olfactory nervous system of Chinook salmon is sensitive to a wide range of dissolved contaminants, and a loss of olfactory capacity could interfere with many important behaviors, incuding feeding, defense, schooling, migration, and reproduction (Scholz and others 2000). The potential occurrence and magnitude of indirect effects associated with contaminants within the Stanislaus River is currently unknown, but studies have been conducted at other locations of concern within the San Joaquin Basin.

Studies of the effects of diazinon on the antipredator behavior of juvenile Chinook parr (47 mm to 63 mm) of hatchery origin, found that concentrations of 1 μg/L and 10.0 μg/L significantly affected antipredator behavior. Concentrations of 0.1 μg/L had no significant effect. Antipredator behavior was evaluated by monitoring changes in feeding behavior when conspecific skin extract was added to the experimental tank. Although no data is available for the Stanislaus River, water quality sampling in the San Joaquin River near Vernalis during winter storms between November and April from 1991 through 1999 detected diazinon in 25% of the samples analyzed. However only 5 % of the samples exceeded diazinon concentrations of 0.294 μg/L, and more than half were less than 0.1 μg/L, so it does not appear that diazinon is a likely problem in the Stanislaus River.

Water samples collected after rainfall events in the San Joaquin River at Vernalis and most other locations in the Delta from January through April in 2001 and 2002 (Werner and others 2003) indicate that the observed concentrations of organophosphate pesticides were seldom toxic to a cladoceran (Ceriodaphnia dubia), a resident cladoceran (Simocephalus vetelus), a chironomid larvae (Chironomus tentans) and an amphipod (Gammarus daiberi). Surveys between 1992 and 2000 suggest that the amounts of organophosphate pesticides applied as dormant sprays in the San Joaquin Basin have steadily decreased over the past decade, although they still exceed criterion maximum concentration levels established by CDFG (Orlando and Kuivila 2003).

Many small agricultural return channels contribute a variety of contaminants to the mainstem San Joaquin River and its tributaries, particularly during the winter when dormant sprays are applied to crops and rain storms flush the contaminants into the rivers in a pulse. However, experimental studies have indicated that there were no detrimental effects of agricultural return flow from the west side of the San Joaquin on the growth and survival of Chinook salmon reared at the Merced Fish Facilities when the return flows were diluted by 50% or more with San Joaquin River water (Saiki and others 1992). Other bioassays with fathead minnows with water samples from the San Joaquin, Merced, Tuolumne, and Stanislaus rivers also showed little evidence of toxicity (Brown 1996). Low or no detectable concentrations of organochlorine pesticides and polychlorinated biphenyls were detected in fish collected from Don Pedro Reservoir on the Tuolumne River, or from the San Joaquin River at Fremont Ford and Mossdale (Goodbred and others 1997).

40


Food Availability and Fall-run Chinook Juvenile Rearing. Chironomidae (midges) are typically cited as an important prey for juvenile Chinook upstream of the Delta (Sasaki 1966; Merz and Vanicek 1996; Moore 1997; Sommer and others 2001b), whereas crustaceans may be more important in the western Delta (Sasaki 1966; Kjelson and others 1982). Juvenile Chinook diets often vary by habitat type, resulting in differences in caloric intake and growth rate (Rondorf and others 1990; Moore 1997; Sommer and others 2001b). However, it remains unclear whether these spatial differences in feeding and growth translate into improved survival (Sommer and others 2001b).

No invertebrate studies have been reported for the lower Stanislaus River in order to determine whether food availability is a limiting factor within the Stanislaus River. However, measurements of muscle lipids were taken from Chinook collected during April and May at the Caswell State Park rotary screw trap to profile the physiological condition of natural Chinook compared with hatchery fish. The percent of muscle lipids found in Stanislaus River juveniles was relatively low compared to naturally produced fish from the Merced and Tuolumne rivers (Nichols and Foott 2002). The low percentage of muscle lipids observed suggests that either food availability or other growth influencing factors were relatively poor in the Stanislaus River during 2001, a dry year, compared to the other two rivers.

It is possible that sedimentation and in-river gravel mining may have a greater impact on the food availability for salmonids in the lower Stanislaus River than in the Merced and Tuolumne rivers. Waters (1995) suggested that a change from gravel and cobble riffles to deposits of silt and sand results not only in a decrease in abundance of invertebrates that are important as fish foods, but also results in a change in invertebrate species from those inhabiting the interstitial spaces of large particles to small, burrowing forms less available to fish. The excavation of gravel and cobbles for in-river mining and high rates of sedimentation from turbid storm runoff in the lower Stanislaus River could have resulted in the loss of interstitial spaces in the substrate and a shift to the small, burrowing species of invertebrates. However, some of the captured mine pits store large volumes of organic matter and contain dense growths of aquatic vegetation which do not appear to reduce the food supply, but likely produces different species of invertebrates than those produced in riffle habitats. An abundant “hatch” of adult aquatic insects has been observed from these ponds and it is possible that they enhance food availability for salmonids compared to the main channels (Walser, personal communication, X).

Most of the energy that drives aquatic food chains in rivers is derived from terrestrial sources (Allan 1995) and aquatic productivity is related to flood magnitude and the area inundated in some rivers (Large and Petts 1996). Flooding, particularly the rising limb of the hydrograph, typically results in high concentrations of both dissolved and particulate organic matter being released into the river (Allan 1995). For example, growth, survival, feeding success and prey availability for juvenile Chinook salmon were higher in the Yolo Bypass, the primary floodplain of the lower Sacramento River, than in the adjacent mainstem channel in 1998 and 1999 (Sommer and others 2001a and b).

The amount of floodplain habitat that is inundated annually has been substantially reduced in the lower Stanislaus River (SRFG 2003), and, as a result, the amount of food available to salmonids may have also been reduced. Most of the remaining floodplain habitat in the lower Stanislaus River consists of short, narrow strips that are inundated at flows of about 1,200 cfs or greater. During outmigration studies, these floodplain areas were inundated most of the time between

41


When?


February and June of 1999 and 2000 when juvenile screw-trap survival estimates were slightly high; whereas, floodplain inundation was limited to a few areas from mid-April to mid-May in 2001 and 2002 when the screw-trap survival estimates were low. It is possible that the floodplain inundation that occurred in 1999 and 2000 resulted in increased food availability which could account for the observed increase in survival. However, analysis of length-weight relationships from individuals captured in the screw traps indicate that, on average, migrating fish between 35 mm and 85 mm (the size at which most Stanislaus River juveniles outmigrate) weighed slightly more at a given length during the dry years of 2001 (n= 2,022), 2002 (n=1,676), and 2003 (n=2,118), than during the wetter conditions of 1999 (n=1,142; Figure 15).

Although this finding appears to contradict the hypothesis that food availability is greater under wetter conditions, other factors may have influenced the observed length-weight relationship. For instance, adult escapement was lower in 1998 than in 2000-2003 which may have reduced the amount of available nutrients that result from decomposing carcasses. If lower escapement in 1998 did result in a substantial reduction in available nutrients, this event could then explain the lower weight versus length for juveniles captured in 1999. Weight data is not available for 2000, nor years prior to 1999.

Figure 15. Relationship of juvenile Chinook weight to fork length based on individuals captured in the Oakdale and Caswell screw traps in 1999, 2001, 2002, and 2003. Weight data are not available from 2000, nor from years prior to 1999.

0

3

6

9

We

igh

t (g

)

30 45 60 75 90 Fork Length (mm)

1999 2001 2002 2003

Length-Weight Relationship for Chinook

42


Another method to compare the possible influence of food availability is annual estimated biomass. This approach is based on the premise that the system can support the food demands of a given mass of individuals, rather than the number of individuals, since food requirements vary with fish size. In the Stanislaus River, biomass was greater in 1999, a higher flow year than 2001 and 2002, which could be interpreted to indicate that food was more available (Figure 16). However, this observation does not take into account the average in-river residence time of individuals. In 1999, the majority of the biomass passing each site consisted of fry that quickly passed through the lower river so food availability in the lower river was of little consequence. However, in 2001 and 2002, food availability would have been of greater importance because fry were not quickly swept through the lower river and would have had the need to seek food resources while in the lower river.

0

750

1,500

2,250

3,000

Bio

mas

s (g

)

1999 2001 2002 2003

Oakdale Caswell

Estimated Annual Chinook Biomass

Figure 16. Estimated annual biomass of juvenile Chinook salmon passing Oakdale and Caswell during 1999, 2001, 2002 and 2003. Weight data are not available from 2000, nor from years prior to 1999 to estimate biomass.

Unscreened Diversions and Fall-run Chinook Juvenile Rearing. There are several small, unscreened diversions primarily located in the lower reaches of the Stanislaus River (Herren and Kawasaki 2001). Although actual entrainment rates at these sites have not been studied, radio tagging studies in the Stanislaus River (see Section 2.1.6, Predation and Fall-run Chinook Juvenile Rearing) did not detect any entrainment of tagged fish at several moderately sized unscreened pumps in the lower river during May and June (Demko and others 1998). Entrainment may have been undetected due to several reasons including (1) the test fish used were larger than most naturally emigrating Chinook juveniles (i.e., approximately 100-125 mm

43


forklength compared to 35-85 mm), and, due to their size, may have been less susceptible to entrainment; (2) only a few study fish were tracked (i.e., less than 50) which may have reduced the odds that individuals would encounter a pumping station; and (3) the operation schedules of the pumps were unknown so fish may have been passing the locations when the pumps were not in operation.

Studies in the Sacramento River and Delta suggest that entrainment rates increase exponentially with increases in diversion rate, but the dominant factor in determining the number of Chinook entrained may be the timing of juvenile Chinook outmigration (Cramer and Demko 1993). In the Sacramento River, studies conducted at six diversion sites during 1992 indicated that the rate of entrainment was highest during the first week of irrigation when pumping was lowest and abundance was highest, but entrainment dropped to near zero when pumping was highest and abundance was lowest. At this time, the schedules and capacities of many pumping stations on the Stanislaus River are unknown so a determination of potential entrainment impacts can not be made.

2.1.7 Fall-run Chinook Salmon Juvenile Migration

Juvenile Fall-run Chinook Migration Requirements

Juvenile salmon migrate downstream to the San Joaquin River and Delta in response to storm runoff and smoltification. Juvenile salmon undergo physiological transformations known as smoltification that adapt them for their transition to salt water (Hoar 1976). These transformations include different swimming behavior and proficiency, lower swimming stamina, and increased buoyancy that also make the fish more likely to be passively transported by currents (Saunders 1965, Folmar and Dickhoff 1980, Smith 1982). Smoltification usually begins in April when the juveniles reach a fork length between 70 and 100 mm. In general, smoltification is timed to be completed as fish are near the fresh water to salt water transition. Environmental factors, such as streamflow, water temperature, photoperiod, lunar phasing, and pollution can affect the onset of smoltification (Rich and Loudermilk 1991). Too long a migration delay after the process begins may cause the fish to miss a biological window of optimal physiological condition for the transition (Walters and others 1978; CDFG 1998c).

The optimal thermal range during smoltification and seaward migration was estimated to be 50°F to 55°F (Boles and others 1988), based largely on studies of steelhead and coho salmon in the Northwest1. Although Chinook salmon can smolt at temperatures as low as 43°F and as high as 68°F, their chances of survival when they first enter seawater is highest at temperatures between 50°F and 63.5°F (Myrick and Cech 2001). If high temperatures prevent juvenile salmon from smolting, the fish must continue to rear in freshwater throughout the summer when temperatures are highest and potentially lethal.

Juvenile emigration is thought to alternate between active movement, resting, and feeding. The amounts of time spent doing each are unknown (CDFG 1998c), but studies have generally shown 1 Note: all temperature requirements given are based on studies conducted outside of the San Joaquin Basin and are often conducted under laboratory conditions using hatchery fish. “Wild” salmon in the San Joaquin Basin may have slightly higher temperature preferences and/or tolerances than those cited. Higher temperature preferences and/or tolerances may be due to adaptation of San Joaquin salmon to naturally higher temperature conditions existing at the southernmost extent of their range and/or due to distinctive differences between “wild” and hatchery fish (CALFED 1999).

44


feeding is most intense during daylight or crepuscular periods (Sagar and Glova 1988). Unpublished rotary screw trap monitoring results from throughout the Central Valley and elsewhere indicate active emigration is most prevalent at night.

Existing Stanislaus River Conditions and Effects on Juvenile Fall-run Chinook Migration

Based on results from fishery and IFIM studies and environmental analyses, streamflow and water temperature appear to be the two primary factors that may influence juvenile fall-run Chinook migration. In addition, predation may be an influencing factor, particularly during dry years.

Streamflow and Juvenile Fall-run Chinook Migration. Based on flow recommendations (Aceituno 1993) which indicate that habitat for juvenile salmonids is greatest at 200 cfs, and temperature modeling (Rowell 1993) data, streamflow releases from Goodwin Dam implemented according to the 1987 agreement between CDFG and USBR are typically adequate to provide suitable water depths, velocities, and water temperature for juvenile salmon migration in the lower Stanislaus River, except perhaps during extremely dry years when the fishery flow allocation is reduced 69,000 acre-feet under a recent variant to the State Water Resources Control Board (SWRCB) Decision 1422.

CDFG Smolt Survival Studies. CDFG has conducted smolt survival studies in the San Joaquin Basin to determine the relationship of survival to river flow under the 1987 agreement with USBR. These studies have included evaluating the survival of large groups of well-fed, hatchery-reared, smolt-sized fish as they migrate between Knights Ferry and the confluence of the Stanislaus and San Joaquin Rivers while flows are held at a relatively stable target for a 7-10 day period. The observed survival rate can provide a good index of density-independent factors that potentially affect migrating smolts, such as entrainment, water temperature, dissolved oxygen, and contaminants, as long as each release group encounters similar conditions (e.g., each group was equally vulnerable to the Mossdale trawling operations and was exposed to similar temperature acclimation conditions during release, and each group encountered both minimal predation and disease infestations). Since these fish were well-fed at the hatchery, food availability would not be expected to affect their short migration time through the river. Due to their readiness to migrate through the system quickly, the availability of rearing space is also unlikely to be an issue. The extent that survival rates may be under- or overestimated due to predation influences is currently unknown. Large groups of hatchery fish may overwhelm predators which would result in underestimating natural predation mortality rates; whereas, many hatchery fish may be more susceptible to predation because they often migrate during the day when predation is greatest (Roper and Scarnecchia 1996) which would result in overestimating natural predation mortality rates.

CDFG conducted hatchery-smolt survival studies in 1986, 1988, 1989, and 2000- 2002. The results of these studies suggest that increasing reservoir releases to more than 600 cfs in April and May only slightly improves the survival of juvenile Merced River Hatchery Chinook salmon between Knights Ferry and the confluence with the San Joaquin River (Figure 17). To estimate juvenile survival, CDFG released two groups of coded wire tagged (CWT) juvenile Chinook from the Merced River Hatchery, one at Knights Ferry and the other at either Naco West or Two Rivers near the mouth of the Stanislaus River. CDFG then recovers the tagged fish with a trawl in the San Joaquin River at Mossdale. During 2001, relatively few CWT fish were recovered at

45


Mossdale with almost twice as many fish released at Knights Ferry recovered than fish released at Two Rivers, so the estimated survival (i.e., 198%) for this year was considered unusual and likely does not reflect the actual survival rate. There are at least two possible explanations for this apparent anomaly: (1) a majority of the Two Rivers release group passed Mossdale when trawling did not occur, whereas a greater proportion of the Knights Ferry release group passed Mossdale when trawling was being conducted; and/or (2) the Two Rivers release group suffered relatively high mortality upon release due to insufficient temperature acclimation (the river temperature being several degrees higher than the transport temperature). The potential magnitude these factors have on influencing survival estimates during other study years is unknown.

0%

25%

50%

75%

100%

Abs

olut

e Su

rviv

al

500 750 1,000 1,250 1,500Goodwin Flow Release (cfs)

8688

89

00

02

Smolt Survival and River Flow

Figure 17. Absolute survival of juvenile Merced River Hatchery Chinook salmon migrating in the lower Stanislaus River between Knights Ferry and the confluence with the San Joaquin River relative to flow releases from Goodwin Dam.

SPC Outmigration Studies. Other studies, using rotary screw traps at Oakdale (RM 40.1) and Caswell State Park (RM 8.6), have been conducted to determine outmigration characteristics of naturally produced fry (<45 mm), parr (45 mm to 79 mm), and smolts (≥80 mm) within the Stanislaus River. The SPC screw trap studies evaluate the survival of naturally produced juveniles as they rear and migrate through the lower river between Oakdale and Caswell State Park. These estimates account for density-independent factors potentially affecting juveniles such as entrainment, water temperature, and dissolved oxygen, as well as density-dependent factors such as food availability, predation, and the bio-energetic suitability of the physical habitat for rearing. However, identifying mortality factors is difficult with these estimates

46


because many habitat factors vary considerably throughout the mid-December to mid-June rearing and migration period. Furthermore, the screw trap survival estimates are highly dependent on accurately estimating trap efficiencies for capturing fry, parr, and smolts over the range of flow and turbidity conditions that fluctuate during the entire sampling period. SPC’s estimates should be reasonably accurate since there is an extensive range of trap efficiency estimates for naturally produced and hatchery fish at both trap locations. Unfortunately, it will not be possible to compare the SPC survival estimates from the first dry year (2001) with escapement-based recruitment estimates until the fall 2004 escapement estimates are available to rebuild the cohort.

These outmigration monitoring studies indicate that survival (i.e., estimated number of juveniles passing Caswell divided by the estimated number of juveniles passing Oakdale) of naturally produced juvenile Chinook (all lifestages) was approximately 95% in 1998, a wet water year; 75% during 1999 and 2000, above-normal water years; but only about 10% during 2001 and 2002, dry water years (Figure 18; SPC 2003). During 1999 and 2000, when flows ranged between 3,000 and 4,500 cfs in February, the screw trap survival index was particularly high for fry. In contrast, during 2001 and 2002, when flows were about 500 cfs in February and March, the survival indices for fry were low.

0%

25%

50%

75%

100%

Cas

wel

l/Oak

dale

1996 1998 1999 2000 2001 2002 2003

Screw Trap Outmigration DifferentialDry YearsWet Years

Figure 18. Estimated survival of naturally produced juvenile Chinook salmon migrating in the lower Stanislaus River between Oakdale and Caswell State Park based on the differences in estimated screw-trap passage estimates.Water Temperature and Juvenile Fall-run Chinook Migration. Peak fall-run Chinook smolt migration in the San Joaquin Basin occurs in April and May. Average daily water temperatures

47


in the Stanislaus River are within the preferred range for smolting (i.e., between 50°F to 55°F) through mid-March at Caswell and Oakdale, and year-round at Knights Ferry, indicating conditions are sufficient for smoltification (Figure 8). As temperatures increase in a downstream direction and increase throughout the entire reach as the season progresses, temperatures above 55°F experienced during migration may act as a migration impediment and may result in fish residualizing and emigrating as yearlings the following spring, particularly in the case of juvenile Chinook migrating through the lower river in June.

CDFG smolt survival studies conducted in the lower Stanislaus River provide two possible scenarios regarding water temperature effects on outmigrating smolts: (1) survival is highest (59%) when the mean daily water temperature at Ripon in April and May was 62°F; or (2) survival was independent of water temperatures below 64°F at Ripon. It is likely that the second conclusion is more appropriate as the range in temperatures tested was only 60°F to 64°F and it is likely that the observed variation in survival estimates was due to other factors or error rather than to small changes in water temperature.

25%

50%

75%

100%

Abso

lute

Sur

viva

l

59 60 61 62 63 64 65Average Temperature (F)

Smolt Survival and Water Temperature

(88)(86)

(89)

(00)

(02)

Figure 19. Absolute survival of juvenile Merced River Hatchery Chinook salmon migrating in the lower Stanislaus River between Knights Ferry and the confluence with the San Joaquin River relative to the mean daily water temperature at Ripon.

Dissolved Oxygen, Predation, Disease, Contaminants, and Unscreened Diversions and Fall-run Juvenile Chinook Migration. Potential influences of dissolved oxygen, predation, disease, contaminants, and unscreened diversions on juvenile fall-run Chinook migration are likely to be

48


similar to those identified for fall-run Chinook juvenile rearing (see Section 2.1.6, Dissolved Oxygen, Predation, Disease, Contaminants, and Unscreened Diversions and Fall-run Chinook Juvenile Rearing).

2.2 SPRING-RUN CHINOOK SALMON

Since spring-run and fall-run salmon have similar habitat requirements for most of their lifecycles, with the exception that spring-run also have summer holding habitat requirements, it is likely that the factors that impact fall-run Chinook salmon within the Stanislaus River, which were discussed in Chapter 2, also impact spring-run Chinook salmon. Since suitable adult summer holding habitat appears to be available, holding habitat conditions are unlikely to limit the spring-run population in the Stanislaus River.

2.2.1 Spring-run Chinook Salmon Population Trends

Spring-run Chinook, which were historically the most numerous race in the Central Valley, have been surpassed in numbers by fall-run Chinook throughout their existing range, and were extirpated from many areas including the San Joaquin Basin by the early 1950’s due to dam construction which blocked access to cool, year-round flows in headwater reaches for spawning, adult holding, and juvenile rearing.

It is likely that spring-run Chinook were abundant in the Stanislaus River prior to hydraulic mining in the watershed and dredging in the Delta during the late 1880s. We can only speculate that their population has not rebounded along with the fall-run Chinook salmon population because the upstream dams currently block the migration of adult fish into headwater reaches of the upper watershed. Historically, spring-run migration into the upper watershed during high spring flow events provided spatial separation from fall-run salmon which were confined to the lower watershed by low fall flows. This spatial separation prevented interbreeding and competition for resources and allowed for development of these distinct races. In addition, upper watersheds likely provided critical habitat for adult spring-run salmon which require deep pools with relatively cold water and overhead cover to oversummer prior to spawning.

In recent years, small numbers of adult salmon (i.e., less than 50) have been observed within the Stanislaus River during June/July which is consistent with spring run upstream migration timing. In 2000, CDFG deployed gill nets at Buttonbush Park (RM 48) on 5 days between June 29 and August 25 to capture some of these returning adults (Guignard 2003). A total of 28 Chinook were captured during the 20 hours sampled and 8 (29%) fish had CWT. The CWT codes indicated that all of the tagged fish were stray fall-run Chinook of Feather River Hatchery origin that had been released as juveniles in the Delta. Although it is impossible to ascertain the origin of the 20 unmarked fish without otolith and/or DNA testing, it is believed that these unmarked adults were also strays from the Feather River hatchery; not all returning hatchery adults are expected to have CWTs since only a proportion of hatchery smolts are tagged each year.

Until we better understand the specific habitat needs of spring-run Chinook salmon and the potential competition for habitat and genetic contamination with fall-run Chinook salmon, we will not know whether a population of spring-run Chinook salmon can re-colonize or be re-introduced to the lower Stanislaus River below Goodwin Dam, and subsequently be sustained in future years.

49


2.2.2 Spring-run Chinook Salmon Life History

Since spring-run were extirpated from the San Joaquin River by the 1950s, there is no specific information regarding “spring-run” observed in the San Joaquin River in recent years, however, monitoring of spring-run in the Sacramento River and its tributaries has documented the life history characteristics of this race within the Sacramento River Basin and Delta.

Spring-run Chinook salmon adults are estimated to leave the ocean and enter the Sacramento River from March to July (Myers and others 1998). This run timing is well adapted for gaining access to the upper reaches of river systems (1,500 to 5,200 feet in elevation) prior to the onset of high water temperatures and low flows that would inhibit access to these areas during the fall. Throughout this upstream migration phase, adults require streamflows sufficient to provide olfactory and other orientation cues used to locate their natal streams. Adequate streamflows are also necessary to allow adult passage to upstream holding habitat in natal tributary streams.

When they enter freshwater, spring-run Chinook salmon are immature and they must stage for several months before spawning. Their gonads mature during their summer holding period in freshwater. Adults prefer to hold in deep pools with moderate water velocities and bedrock substrate and avoid cobble, gravel, sand, and especially silt substrate in pools (Sato and Moyle 1989).

Spawning typically occurs between late-August and early October with a peak in September. Once spawning is completed, adult spring-run Chinook salmon die. Length of time required for eggs to develop and hatch is dependant on water temperature and is quite variable, however, hatching generally occurs within 40 to 60 days of fertilization (Vogel and Marine 1991). In Deer and Mill creeks, embryos hatch following a 3-5 month incubation period (USFWS 1995). After hatching, pre-emergent fry remain in the gravel living on yolk-sac reserves for another two to four weeks until emergence. Timing of emergence within different drainages is strongly influenced by water temperature. Emergence of spring-run Chinook typically occurs from November through January in Butte and Big Chico Creeks and from January through March in Mill and Deer Creeks (CDFG 1998c).

Post-emergent fry seek out shallow, nearshore areas with slow current and good cover, and begin feeding on small terrestrial and aquatic insects and aquatic crustaceans. As they grow to 50 to 75 mm in length, the juvenile salmon move out into deeper, swifter water, but continue to use available cover to minimize the risk of predation and reduce energy expenditure.

In Deer and Mill creeks (tributaries to the Sacramento River), juvenile spring-run Chinook spend 9-10 months rearing within theses streams during most years, with some spending as long as 18 months in freshwater before migrating downstream. Most of these “yearling” spring-run Chinook move downstream during the first high flows of their second winter which can occur from November through January (USFWS 1995; CDFG 1998c). In Butte and Big Chico creeks, spring-run Chinook juveniles typically exit their natal tributaries soon after emergence during December and January, while some remain throughout the summer and exit the following fall as yearlings. In the Sacramento River and other tributaries, juveniles may begin migrating downstream almost immediately following emergence from the gravel with emigration occurring from December through March (Moyle and others 1989, Vogel and Marine 1991).

50


Chinook salmon spend between one and four years in the ocean before returning to their natal streams to spawn (Myers and others 1998). Fisher (1994) reported that 87% of returning spring-run adults in the Sacramento River are three-years-old based on observations of adult Chinook trapped and examined at Red Bluff Diversion Dam between 1985 and 1991.

2.2.3 Spring-run Chinook Salmon Adult Upstream Migration

Spring-run Chinook Adult Upstream Migration Requirements

Adult migration requirements for spring-run Chinook are similar to fall run (see fall-run adult migration requirements under Section 2.1.3, Fall-run Chinook Salmon Adult Upstream Migration) with the exception of difference in migration timing.

Existing Stanislaus River Conditions and Effects on Spring-run Chinook Adult Upstream Migration

Based on the assumption that factors affecting fall-run will likely affect spring-run in a similar way, it appears that spring-run Chinook adult upstream migration opportunities are suitable in the Stanislaus River.

Streamflow and Spring-run Chinook Adult Upstream Migration. Stanislaus River flows during most of the adult spring-run Chinook upstream migration period (late winter and spring) provide suitable water depths, velocities, and water temperatures for adult passage to existing spawning grounds.

Water Temperature and Spring-run Chinook Adult Upstream Migration. As mentioned previously, maximum daily average water temperature in the Stanislaus River at Caswell has been monitored since 1998. Average maximum daily water temperatures at Caswell during the early months of the spring-run Chinook migration period (March through mid-June) are suitable for migration. However, temperatures during the latter migration months (mid-June through July) typically exceed 65°F at Caswell and occasionally exceeded 65°F at Oakdale, but remain below lethal limits (Figure 7). During these latter migration months, egg viability of spring-run adult migrants traveling through the lower reaches of the Stanislaus River could be reduced. The potential for reduced egg viability during this period is not unique to the Stanislaus River. Temperatures throughout the Delta and lower reaches of other tributaries are similar at this time, so any salmon migrating during the summer months are likely to experience some degree of reduced egg viability during their migration through the Delta and into at least the lower reaches of spawning tributaries.

Dissolved Oxygen and Spring-run Chinook Adult Upstream Migration. As mentioned previously, DO measurements have been recorded hourly at Ripon and have encompassed a range of water year types and corresponding flows (dry to wet years with low to high flows, respectively). The minimum average daily DO (i.e., the lowest average DO value recorded on a particular date for the period of record) at Ripon has generally ranged from 7 to 10, and only fell below 5 mg/L on three days during the spring-run migration period during the four years of monitoring (Figure 8) indicating that DO in the Stanislaus River is not likely to be a problem for upstream migrants.

51


Passage and Spring-run Chinook Adult Upstream Migration. As mentioned previously, Goodwin Dam is the first impassable barrier in the Stanislaus River that fish traveling upstream from the San Joaquin River encounter. This dam prevents adult salmonids from entering the historically accessible upper river and headwater reaches. Unlike fall-run Chinook, there are no historical accounts available regarding spring-run spawning distribution to determine the actual amount of spawning habitat lost due to Goodwin Dam and other dams immediately upstream such as Tulloch and New Melones. It is known that spring-run Chinook historically accessed much higher elevations than fall-run for spawning and that these dams have prevented access to most, if not all, of historical spring-run habitat. Currently, there are no physical passage barriers below Goodwin Dam to limit upstream passage of spring-run Chinook to available spawning areas and flows are adequate for maintaining upstream passage opportunities once fish have entered the river.

Poaching and Spring-run Chinook Adult Upstream Migration. Under current CDFG regulations for the Stanislaus River, fishing is legal during the spring-run adult upstream migration, but there is a zero bag limit for Chinook salmon. Although CDFG regulations limit the impacts of fishing on migrating salmon, CDFG has indicated that poaching (i.e., illegal harvest) of adult Chinook salmon in the Stanislaus River likely occurs. However, no information is currently available regarding the extent of poaching and the magnitude of spring-run adult migrant loss due to poaching can not be estimated at this time. It should be noted that there are few spring-run Chinook in the Stanislaus River so poaching may be unlikely, however spring-run may be more susceptible to poaching than fall-run Chinook due to their extended holding time before spawning and because fishing is legal during their upstream migration and holding period.

2.2.4 Spring-run Chinook Salmon Adult Holding Habitat

Spring-run Chinook Adult Holding Requirements

Over-summering spring-run adults require cold-water refuges such as deep pools to conserve energy for gamete production, redd construction, spawning, and redd guarding. CDFG (1998a) describes quality spring-run holding habitat as consisting of (1) deep pools, (2) adequate cover, such as bubble curtains created by flowing water, (3) proximity to spawning gravel, and (4) adequate water temperatures and DO concentrations. The upper limit of the optimal temperature range for adults holding while eggs are maturing is 59°F to 60°F (Hinze 1959). Unusual stream temperatures during spawning migration and adult holding periods can alter or delay migration timing, accelerate or retard mutations, and increase fish susceptibility to diseases. Sustained water temperatures above 80.6°F are lethal to adults (Cramer and Hammack 1952; CDFG 1998c).

Optimal water velocities for adult Chinook salmon holding pools range between 0.5-1.3 feet-per-second and depths are at least three to ten feet (G. Sato unpublished data; Marcotte 1984). The pools typically have a large bubble curtain at the head, underwater rocky ledges, and shade cover throughout the day (Ekman 1987).

Existing Stanislaus River Conditions and Effects on Spring-run Chinook Adult Holding

52


Spring-run Chinook holding habitat currently exists at numerous sites in Goodwin Canyon and four small captured mined pits near Lovers’ Leap (RM 53.3), Willms Pond (RM 51.8), and Button Bush Park (RM 48). Although the long deep pools in Goodwin Canyon do not contain spawning gravel, a few adult Chinook were observed holding there in summer 2000 (Fisheries Foundation 2002). Based on the number of holding habitats available, it is highly unlikely that the quantity of adult holding habitat currently limits the spring-run population in the Stanislaus River. As documented below, streamflow and DO also appear to be suitable. Water temperatures and recreational use have the potential to adversely impact holding adults, but the potential magnitude of these impacts is unknown.

Streamflow and Spring-run Chinook Adult Holding. Mean daily flows at the Orange Blossom Bridge (DWR gage) were usually greater than 200 cfs from June through September between 1991 and 2001; however, flows were near 110 cfs for about 45 days during summer 1991. An IFIM study conducted in 1989 (Aceituno 1993) did not identify instream flows needed for adult migration or holding.

Water Temperature and Spring-run Chinook Adult Holding. USBR has developed a Stanislaus River Basin Water Temperature Model (Rowell 1993) to predict mean water temperatures within a few degrees based on flow releases, as well as corresponding flow release temperatures, from Goodwin Dam. For example, at a base flow of 200 cfs, weekly mean water temperatures at the Orange Blossom Bridge are predicted to range between 59.5 and 66.8°F from June through September when the temperature of releases from Goodwin dam are moderate. Based on temperature predictions according to this model, it is expected that temperatures below 65°F can be provided between Goodwin Dam and OBB during the summer for juvenile steelhead rearing in most years. Therefore, NOAA Fisheries has provided a term and condition in a Biological Opinion (NOAA Fisheries 2002), which states that USBR shall, to the extent possible, control water temperatures by flow releases to the lower river between Goodwin Dam (RM 58.5) and Orange Blossom Road Bridge (USGS Gauge) during June 1 through November 30, to a daily average temperature of less than or equal to 65°F to protect over-summering steelhead from thermal stress and from warm water predator species. This summer temperature requirement offers the added benefit of providing adequate temperature conditions for spring-run adults holding in habitats further upstream.

Hourly summer temperatures measured at the Orange Blossom Bridge (DWR gage; RM 46.9) during 2001 fit within predicted weekly water temperatures, and ranged between 55°F and 65°F at flows between 287 and 840 cfs. Several holding habitat sites are located upstream of OBB where temperatures are expected to be cooler. Since summer flows during recent years have been greater than 200 cfs, with the exception of 1991 when flows dropped to 110 cfs for about 45 days, it is likely that summer water temperatures have been suitable above OBB for holding adult spring-run salmon, with the exception 1991.

In addition, maximum daily average temperatures at Knight’s Ferry (RM 54.5) between 1998 and 2002 indicate that temperatures have been below 59°F under a variety of water years types. Therefore, it is likely that temperatures do not adversely impact egg viability of adults holding in Knight’s Ferry pool areas during most, if not all, years. However, adults holding in pools near Frymire Ranch (RM 53.4), Willms Pond (RM 51.8), and Button Bush Park (RM 48) may experience reduced egg viability, but the magnitude of this loss is currently unknown.

53


Dissolved Oxygen and Spring-run Chinook Adult Holding. As mentioned previously, DO measurements have been recorded hourly at Ripon and have encompassed a range of water year types and corresponding flows (dry to wet years with low to high flows, respectively). The minimum average daily DO (i.e., the lowest average DO value recorded on a particular date for the period of record) at Ripon has generally ranged from 7 to 10, and only fell below 5 mg/L on three days during the spring-run holding period during the four years of monitoring (Figure 8) indicating that DO in the Stanislaus River is not likely to be a problem for holding adults.

Recreation and Spring-run Chinook Adult Holding. Spring-run tend to be easily disturbed and stressed by instream and streamside movement which increases the importance of cover for oversummering adults, particularly deep pools for holding habitat. Since spring-run hold in cool pools for extended periods during the summer, they are more likely to encounter harassment stress associated with people engaging in recreational activities than other Chinook. The potential magnitude of harassment stress and its possible associated impacts, such as reduced egg viability, is currently unknown. 2.2.5 Spring-run Chinook Salmon Spawning

Spring-run Chinook Spawning Requirements

Adult spawning requirements for spring-run Chinook are similar to fall-run (see Section 2.1.4, Fall-run Chinook Spawning Requirements) with the exception of differences in optimal substrate preferences and spawn timing. Optimum substrate for spring-run embryos is a mixture of gravel and cobble with a mean diameter of one to four inches with less than 5% fines, which are less than or equal to 0.3 inches in diameter (Platts and others 1979, Reiser and Bjornn 1979). Although most spring and fall-run spawning does not occur at the same time, a portion of their spawning activity can temporally overlap for several weeks during early October which leads to potential hybridization between the races wherever they are not spatially separated due to loss of headwater access by spring-run.

Existing Stanislaus River Conditions and Effects on Spring-run Chinook Spawning

No systematic surveys have been conducted for the small number of phenotypic “spring-run” fish observed entering the Stanislaus River in recent years. However, spring-run and fall-run spawning and spawning habitat requirements are similar so it is assumed that factors affecting fall-run will likely affect spring-run in a similar way. Based on this assumption, there appear to be several factors that may influence spring-run Chinook spawning and spawning habitat in the Stanislaus River including limited spawning gravel supplies; substrate armoring and embeddedness; and increased turbidity levels. Spawning habitat has been altered as a result of reduced gravel recruitment due to gravel mining and blockage of sediments and reduced sediment transport flows caused by dams, and changes in streamside land use (see Section 2.1.4, Existing Stanislaus River Conditions and Effects on Fall-run Chinook Spawning).

Spawning Habitat Distribution. Unlike fall-run Chinook, there are no historical accounts available regarding spring run spawning distribution to determine the actual amount of spawning habitat lost due to Goodwin Dam and other dams immediately upstream such as Tulloch and New Melones. It is known that spring-run Chinook historically accessed much higher elevations than fall-run for spawning and that these dams have prevented access to most, if not all, of

54


historical spring-run habitat. Today, fall-run Chinook spawning typically occurs between Goodwin Dam (RM 58.3) and Jacob Meyers Park in Riverbank (RM 33) at about 120 natural riffles and it is assumed that spring-run would spawn in the same areas.

Preferred Spawning Areas. Unlike fall-run Chinook, there is no information available regarding specific preferred spawning areas for spring-run Chinook because the number of phenotypic “spring-run” has been few, and redd surveys do not begin until the last few weeks of the typical spring-run spawning period. Due to overlap in timing, redd surveys cannot distinguish spring-run redds from fall-run redds. However, observations of spring-run spawning in other Central Valley tributaries, such as the Feather River, indicate that fish, particularly those that arrive earlier in the season, typically spawn in the uppermost reaches of available spawning habitat. On the Stanislaus River, it is anticipated that spring-run would behave similarly and would spawn in the uppermost reaches below Goodwin Dam.

Armoring and Embeddedness, and Turbidity. Since spring-run spawning requirements are similar to fall-run Chinook, effects of existing conditions on spring-run spawning and spawning habitat are presumed to be similar to those identified for fall-run Chinook (See Section 2.1.4, Armoring and Embeddedness and Fall-run Chinook Salmon Spawning; and Turbidity and Fall-run Chinook Salmon Spawning). However, the overall percentage of spring-run redds may experience higher rates of redd superimposition (i.e., a new redd is built over a pre-existing redd) than fall-run Chinook due to two factors: (1) spring-run escapement is very low (less than a few hundred fish), and (2) the increased likelihood that spring-run redds will be disturbed/destroyed by fall-run salmon spawning activities since spring-run spawn earlier (September and October) than fall-run (late-October to December) and fall-run are more numerous. Redd superimposition of any existing spring-run redd would likely either entomb spring-run alevins by burying them with silt and sand or kill a number of spring-run eggs.

In fall 2000, fall-run escapement was relatively high at approximately 8,500 fish and redd superimposition during this time was observed at artificial redds previously constructed during the spring-run spawning period (September and October). These artificial redds were located between Knights Ferry and Willms Pond (CMC 2002b) and 33% of their egg pockets were completely disturbed while another 21% were buried by fall-run spawning. Although escapement and corresponding superimposition rates were relatively high in 2000, redd superimposition rates may also be high when escapement is relatively low due to the fact that salmon prefer to spawn in easily moveable, appropriately sized gravel, as occurs in recently constructed redds in the highly compacted, natural spawning sites of the Stanislaus River. In fall 1996, fall run escapement was relatively low at approximately 750 fish, yet redd superimposition completely disturbed 24% of the egg pockets of salmon redds marked with pipe piezometers over an eight-day period in mid November (Mesick 2001a). Redd superimposition by fall-run salmon may destroy 40% to 50% of the spring-run eggs each year, which coupled with an extremely low number of spawners, and only a small fraction of eggs surviving to adulthood make recovery of spring-run in the Stanislaus River unlikely in the absence of restoration efforts.

2.2.6 Spring-run Chinook Salmon Incubation and Emergence

Spring-run Chinook and Emergence Requirements

55

michele simpson, 03/10/04,

This has been mentioned several times in meetings we have attended, but we have no documentation. Is anyone aware of a reference we can cite?


Incubation requirements for spring-run Chinook are similar to fall-run (see Section 2.1.5, Fall-run Chinook Salmon Incubation and Emergence) with the exception of difference in timing of incubation periods.

Existing Stanislaus River Conditions and Effects on Spring-run Chinook Incubation and Emergence

No systematic surveys have been conducted for the small number of phenotypic “spring-run” fish observed entering the Stanislaus River in recent years. However, spring-run and fall-run incubation and incubation habitat requirements are similar so it is assumed that factors affecting fall-run will likely affect spring-run in a similar way. Based on this assumption, spring-run Chinook egg incubation and incubation habitat in the Stanislaus River could be influenced by high concentrations of fines within spawning gravels that result in low DO levels, as well as streamflow. Water temperatures appear to be suitable for spring-run Chinook incubation.

Fines and Dissolved Oxygen, and Spring-run Chinook Incubation and Emergence. Since spring-run incubation requirements are similar to fall-run Chinook, effects of existing fines and DO conditions on spring-run incubation and incubation habitat would be similar to fall-run Chinook (see Section 2.1.5, Fines and Dissolved Oxygen and Fall-run Chinook Incubation and Emergence). However, the overall percentage of spring-run redds may experience higher rates of fine deposition than fall-run Chinook due to two factors: (1) spring-run escapement is very low (less than a few hundred fish), and (2) the increased likelihood that spring-run redds will be disturbed/destroyed by fall-run salmon spawning activities since spring-run spawn earlier (September and October) than fall-run (late-October to December) and fall-run are more numerous.

Streamflow and Spring-run Chinook Incubation and Emergence. Since spring-run incubation requirements are similar to fall-run Chinook, effects of streamflow on spring-run incubation and incubation habitat would be similar to fall-run Chinook (see Section 2.1.5, Streamflow and Fall-run Chinook Incubation and Emergence).

Water Temperature and Spring-run Chinook Incubation and Incubation Habitat. Thermograph data collected since 1998 indicates that maximum average daily water temperatures were below 58°F at Knight’s Ferry and below 65°F at Oakdale during most of the spring-run Chinook incubation and emergence period (These previously identified thermaltolerances and blockage temperatures do not appear to reflect fish survival and behaviorobserved under “natural” field conditions within the Stanislaus River. For example, althoughincipient lethal temperatures have been identified as 69.8°F (Houston 1982; Coutant 1970) andradio tracking studies performed in the lower San Joaquin/Delta (Hallock and others 1970) andelsewhere such as Washington (Bumgarner and others 1997) and Idaho (Stabler 1981) haveindicted that adult upstream migration becomes blocked at about 70°F, recent observations ofadult salmon passage in the Stanislaus River during a demonstration weir project in 2003indicate that fish had to migrate for prolonged periods at average daily water temperatures above70°F (Figure 6) in the Delta and lower San Joaquin to reach the weir site.Turbidity and Spring-run Chinook Incubation and Incubation Habitat. Spring-run incubating eggs hatch and alevins emerge by December which makes them less susceptible to turbidity effects because increased turbidity is primarily associated with intensive turbid storm

56


runoff events that do not usually occur until mid- to late January in the Stanislaus River. Therefore, potential turbidity effects on incubating spring-run are not anticipated.

2.2.7 Spring-run Chinook Salmon Juvenile Rearing

Spring-run Chinook Juvenile Rearing Requirements

Rearing requirements for spring-run Chinook are presumed to be similar to fall-run (see Section 2.1.6, Fall-run Chinook Juvenile Rearing Requirements) with the exception of differences in timing of rearing periods.

Existing Stanislaus River Conditions and Effects on Spring-run Chinook Juvenile Rearing and Rearing Habitat

Changes in land use, the frequency and magnitude of natural disturbances, and the development of water, hydroelectric and flood control projects are presumed to have impacts on spring-run Chinook juveniles similar to those on fall-run Chinook juveniles (see Section 2.1.6., Existing Stanislaus River Conditions and Effects on Fall-run Chinook Juvenile Rearing and Rearing Habitat). However, spring-run juveniles emerge before fall-run juveniles so they likely have a competitive advantage for exploiting the best available rearing habitat which may reduce the magnitude of impacts compared to fall-run juveniles. Nonetheless, relatively few spring-run sized juveniles are ever captured in rotary screw trap sampling which indicates that other factors besides juvenile habitat suitability probably are limiting the spring-run Chinook salmon population.

Water Temperature and Spring-run Chinook Juvenile Rearing. Adherence to water quality standards for temperature and DO within the Stanislaus River and Delta ensure that water temperatures in the Stanislaus River are maintained within a suitable range for juvenile spring-run rearing (Figure 10). On average, maximum daily water temperatures are between 50o F and 60o F from December through May in the entire river and year-round above Knights Ferry. Based on the limited number of spring-run sized fish in the screw traps, it appears that juveniles emigrate prior to March so rearing temperatures would be suitable.

Streamflow, Dissolved Oxygen, Predation, Disease, Food Availability, Contaminants, and Unscreened Diversions and Spring-run Chinook Salmon Juvenile Rearing. Potential influences of streamflow, dissolved oxygen, predation, disease, food availability, contaminants, and unscreened diversions on juvenile spring-run Chinook rearing are likely to be similar to those identified for fall-run Chinook juvenile rearing (see Section 2.1.6, Streamflow and Fall-run Chinook Juvenile Rearing; Dissolved Oxygen and Fall-run Chinook Juvenile Rearing; Predation and Fall-run Chinook Juvenile Rearing; Disease and Fall-run Chinook Juvenile Rearing; Food Availability and Fall-run Chinook Juvenile Rearing; Contaminants and Fall-run Chinook Juvenile Rearing; and Unscreened Diversions and Fall-run Chinook Juvenile Rearing).

2.2.8 Spring-run Chinook Salmon Juvenile Migration

Juvenile Spring-run Chinook Migration Requirements

57


Juvenile migration requirements for spring-run Chinook are presumed to be similar to fall-run (see Section 2.1.7, Fall-run Chinook Juvenile Migration Requirements) with the exception of differences in timing of migration periods.

Existing Stanislaus River Conditions and Effects on Juvenile Fall-run Chinook Migration

Since spring-run Chinook juvenile migration requirements are similar to fall-run Chinook and impacts are expected to be similar, there are two primary factors that may influence juvenile spring-run Chinook migration including streamflow and water temperature. In addition, predation may be an influencing factor, particularly during dry years.

Water Temperature and Spring-run Chinook Juvenile Migration. Spring-run juveniles begin their downstream outmigration slightly earlier than fall-run juveniles when water temperatures, and presumably corresponding temperature-related mortality rates, would be lower. Therefore, it is unlikely that temperature conditions affecting the survival of migrating juveniles account for the relatively low number of juvenile spring-run salmon migrants compared to the number of fall-run salmon migrants in the Stanislaus River.

Streamflow, Dissolved Oxygen, Predation, Disease, Contaminants, and Unscreened Diversions and Spring-run Chinook Migration. Potential influences of streamflow, dissolved oxygen, predation, disease, contaminants, and unscreened diversions on juvenile spring-run Chinook migration are likely to be similar to those identified for fall-run Chinook juvenile migration (see Section 2.1.7, Dissolved Oxygen and Fall-run Chinook Juvenile Migration; Predation and Fall-run Chinook Juvenile Migration; Disease and Fall-run Chinook Juvenile Migration; Contaminants and Fall-run Chinook Juvenile Migration; and Unscreened Diversions and Fall-run Chinook Juvenile Migration).

2.3 STEELHEAD

2.3.1 Steelhead Population Trends

Central Valley steelhead once ranged throughout most of the tributaries and headwaters of the Sacramento and San Joaquin basins prior to dam construction, water development, and watershed perturbations of the 19th and 20th centuries (McEwan and Jackson 1996). Historical documentation exists that show steelhead were once widespread throughout the San Joaquin River system (CALFED 1999). In the early 1960s, the California Fish and Wildlife Plan estimated a total run size of about 40,000 adults for the entire Central Valley including San Francisco Bay (CDFG 1965). The annual run size for the Central Valley Evolutionary Significant Unit (ESU) in 1991-92 was probably less than 10,000 fish based on dam counts, hatchery returns and past spawning surveys (McEwan and Jackson 1996).

Estimates of steelhead historical habitat can be based on estimates of salmon historical habitat. The extent of habitat loss for steelhead is probably greater than losses for salmon, because steelhead go higher into the drainages than do Chinook salmon (Yoshiyama and others 1996). Clark (1929) estimated that originally there were 6,000 miles of salmon habitat in the Central Valley system and that 80% of this habitat had been lost by 1928. Yoshiyama and others (1996) calculated that roughly 2,000 miles of salmon habitat was actually available before dam construction and mining, and concluded that 82% of what was present is not accessible today.

58


Clark (1929) did not give details about his calculation. Whether Clark’s or Yoshiyama’s calculation is used, only remnants of the former steelhead range remain accessible today in the Central Valley.

As with Central Valley spring-run Chinook, impassable dams block access to most of the historical headwater spawning and rearing habitat of Central Valley steelhead. In addition, much of the remaining, accessible spawning and rearing habitat is severely degraded by elevated water temperatures, agricultural and municipal water diversions, unscreened and poorly screened water intakes, restricted and regulated streamflows, levee and bank stabilization, and poor quality and quantity of riparian and shaded riverine aquatic (SRA) cover.

At present, wild steelhead stocks appear to be mostly confined to the upper Sacramento River tributaries such as Antelope, Deer, and Mill creeks and the Yuba River (McEwan and Jackson 1996). Naturally spawning populations are also known to occur in Butte Creek, and the upper Sacramento, Feather, American, Mokelumne, and Stanislaus rivers.

Until 2003, the only O. mykiss monitoring which occurred in the Stanislaus River was bi-weekly snorkeling surveys and rotary screw trap sampling. Downstream migrating juvenile O. mykiss, have been captured between December and July in the Stanislaus River rotary screw traps (Figure 20). Most captured individuals are presumed to be steelhead based on their smolting index (smolt index 5). Due to the threatened status of steelhead, mark-recapture tests have not been performed. Instead, annual indices of abundance were calculated by expanding rotary screw trap catches based on the proportion of flow sampled by the trap. The expanded data was then standardized for sampling period. Indices of juvenile O. mykiss abundance since 1996 were similar between years and ranged from 101 to 297, with the exception of 1999 when the abundance index was 894 (Figure 21).

During the spring of 2003, the Stanislaus River Weir was installed and monitored near Riverbank to evaluate returning adult steelhead abundance. During 25 days of sampling between January 27 and March 7, no steelhead were captured in the trap. However, it was determined in fall 2003 that the trap design was ineffective at retaining fish so it is possible that steelhead entered the trap but then exited undetected. It is also possible that steelhead passed the weir on days when trapping did not occur since sampling was not continuous. The trap was modified to increase retention rates during the fall of 2003 and an infrared counting device was installed to monitor steelhead passage at the weir on days when trapping does not occur. This effort is expected to provide more insight regarding steelhead escapement during the winter and spring of 2004.

During weir operations in 2003, three O. mykiss carcasses (22 inches, 21 inches, and 17 inches) washed up on the weir. The carcasses were collected and provided to CDFG for scale, otolith, and tissue analyses to determine age, life history, and relatedness to other Central Valley populations. Analysis of the collected samples has not yet begun and results are expected no earlier than spring 2004.

59


Figure 20. Individual lengths of O. mykiss captured in the Oakdale and Caswell rotary screw traps from 1995 through 2003.

0

100

200

300

400

500

Fo

rkle

ng

th (

mm

)

12-Dec 16-Jan 20-Feb 27-Mar 01-May 05-Jun 10-Jul

Individual O. mykiss Lengthsat Caswell and Oakdale, 1995-2003

0

250

500

750

1,000

Es

tim

ate

d P

as

sa

ge

1996 1998 1999 2000 2001 2002 2003

Estimated O. mykiss Passageat Oakdale

60


Figure 21. Annual estimated O. mykiss passage at Oakdale from 1996 through 2003. Passage estimates are catch expanded for the estimated proportion of flow sampled by the trap.

2.3.2 Steelhead Life History

All Central Valley steelhead are currently considered winter-run steelhead (McEwan and Jackson 1996), although there are indications that summer steelhead were present in the Sacramento River system prior to the commencement of large-scale dam construction in the 1940's (IEP 1999). Adult steelhead migrate upstream in the Sacramento River mainstem from July through March, with peaks in September and February (Bailey 1954; Hallock and others 1961). The timing of upstream migration is generally correlated with higher flow events, such as freshets or sand bar breaches, and associated lower water temperatures.

Spawning may begin as early as late December and can extend into April with peaks from January through March (Hallock and others 1961). Fly fishermen report that steelhead frequently congregate in the upper spawning reaches of the Stanislaus River in January and February, a possible indication of the peak spawning period for the Stanislaus River (John Murphy, California Trout, personal communication as cited in CALFED 1999). Unlike Chinook salmon, not all steelhead die after spawning. Some may return to the ocean and repeat the spawning cycle for two or three years; however, the percentage of repeat spawners is generally low (Busby and others 1996).

After hatching, pre-emergent fry remain in the gravel living on yolk-sac reserves for another four to six weeks, but factors such as redd depth, gravel size, siltation, and temperature can speed or retard this time (Shapovalov and Taft 1954). Upon emergence, steelhead fry typically inhabit shallow water along perennial stream banks. Older fry establish territories which they defend

61


(Shapovalov and Taft 1954). Streamside vegetation is essential for foraging, cover, and general habitat diversity. Steelhead juveniles are usually associated with the bottom of the stream. In winter, they become inactive and hide in available cover, including gravel or woody debris (NOAA 2002).

After spending one to three years in freshwater, juvenile steelhead migrate downstream to the ocean. Most Central Valley steelhead migrate to the ocean after spending two years in freshwater (Hallock and others 1961, Hallock 1989). Barnhart (1986) reported that steelhead smolts in California range in size from 14 to 21 cm (fork length). In preparation for their entry into a saline environment, juvenile steelhead undergo physiological transformations known as smoltification that adapt them for their transition to salt water. These transformations include different swimming behavior and proficiency, lower swimming stamina, and increased buoyancy that also make the fish more likely to be passively transported by currents (Saunders 1965, Folmar and Dickhoff 1980, Smith 1982). In general, smoltification is timed to be completed as fish are near the fresh water to salt water transition. Too long a migration delay after the process begins is believed to cause the fish to miss the “biological window” of optimal physiological condition for the transition (Walters and others 1978). Hallock and others (1961) found that juvenile steelhead in the Sacramento Basin migrated downstream during most months of the year, but the peak period of emigration occurred in the spring, with a much smaller peak in the fall.

Steelhead spend between one and four years in the ocean (usually one to two years in the Central Valley) before returning to their natal streams to spawn (Barnhart 1986; Busby and others 1996).

2.3.3 Steelhead Adult Upstream Migration

Steelhead Adult Upstream Migration Requirements

The preferred temperatures for steelhead upstream migration observed outside of the San Joaquin Basin are between 46F and 52F (Reiser and Bjornn 1979, Bovee 1978, Bell 1986) and could be lower than the temperatures actually preferred in the Stanislaus River. Unusual stream temperatures during upstream migration periods can alter or delay migration timing, accelerate or retard mutations, and increase fish susceptibility to diseases (NOAA Fisheries 2000). The minimum water depth necessary for successful upstream passage is 18 cm (Thompson 1972). Velocities of 3-4 meters per second approach the upper swimming ability of steelhead and may retard upstream migration (Reiser and Bjornn 1979) if areas of lower velocity are not available in the channel.

Existing Stanislaus River Conditions and Effects on Steelhead Adult Upstream Migration

Based on environmental data and fishery studies discussed below, it appears that steelhead adult upstream migration opportunities are suitable in the Stanislaus River.

Streamflow and Steelhead Adult Upstream Migration. Stanislaus River flows during a majority of, including the peaks of, steelhead adult upstream migration period provide suitable water depths and velocities for adult passage to existing spawning grounds.

Water Temperature and Steelhead Adult Upstream Migration. Maximum daily average water temperature in the Stanislaus River at Caswell has been monitored since 1998. The

62


Caswell monitoring station is located at the furthest point downstream and temperatures are the highest at this location compared to temperatures near actual spawning grounds. During the steelhead migration period, maximum average daily water temperatures at Caswell are generally below 55°F from the end of November through early March, are between 55 and 65°F through the end of May, and are above 65°F through the end of summer (Figure 22). These temperatures during the majority of the steelhead upstream migrating period are not expected to adversely impact adults. However, any adults attempting to migrate during the summer months may experience reduced egg viability.

Figure 22. Average maximum daily temperatures at Caswell, Oakdale, and Knights Ferry, 1998-2003, and adult steelhead requirements.

Dissolved Oxygen and Steelhead Adult Upstream Migration. As mentioned previously, DO measured at Ripon since 1999 indicates that the minimum average daily DO (i.e., the lowest average DO value recorded on a particular date for the period of record) at Ripon has generally ranged from 7 to 11, and only fell below 5 mg/L on three days during the steelhead migration period during the four years of monitoring (Figure 8) indicating that DO in the Stanislaus River is not likely to be a problem for upstream migrants.

Passage and Steelhead Adult Upstream Migration. As mentioned previously, Goodwin Dam is the first impassable barrier in the Stanislaus River that fish traveling upstream from the San Joaquin River encounter. This dam prevents adult salmonids from entering the historically

35

45

55

65

75

85

Te

mp

era

ture

(F

)

01-Jan03-Feb

07-Mar09-Apr

12-May14-Jun

17-Jul19-Aug

21-Sep24-Oct

26-Nov29-Dec


Average Maximum Daily TemperatureAnd Steelhead Requirements

JuvenilePreferredRange

Egg Incub.And AdultMigrationPreferredRange

PreferredRange forSpawning

63


accessible upper river and headwater reaches. Unlike fall-run Chinook, there are no historical accounts available regarding steelhead spawning distribution to determine the actual amount of spawning habitat lost due to Goodwin Dam and other dams immediately upstream such as Tulloch and New Melones. Steelhead were likely impacted more significantly than Chinook populations by the reduction of available spawning and rearing habitat from dam construction since a significant portion of their historical, headwater habitat was made inaccessible. Historically, a stream-maturing steelhead population occurred within the Sacramento/San Joaquin Basin, but this population has been replaced by an ocean-maturing type (McEwan 2001). This shift from stream-type to ocean-type steelhead may be the result of dam construction that blocked access to headwater reaches; stream-type steelhead may have required habitat conditions found only in these headwater reaches, whereas, ocean-type steelhead may be better suited for, or have adapted quickly to, habitat conditions found in lower river reaches such as downstream of Goodwin Dam. Currently, there are no physical passage barriers below Goodwin Dam to limit upstream passage of steelhead to available spawning areas and flows are adequate for maintaining upstream passage opportunities once fish have entered the river

Instream Harvest and Steelhead Adult Upstream Migration. Under current California Department of Fish and Game (CDFG) fishing regulations for the Stanislaus River, no fishing is allowed from October 15 through December 31 which encompasses a portion of steelhead upstream migration, and there is a catch-and-release steelhead fishery in the lower Stanislaus River between January 1 and October 15 which may adversely affect steelhead due to handling stress. Artificial lures with barbless hooks are required between Goodwin Dam and the Highway 120 Bridge in Oakdale and bait fishing is allowed downstream of the Highway 120 Bridge. Bait fishing downstream of Highway 120 potentially results in the capture of migrating steelhead.

The potential for hooking mortality of adult steelhead has not been studied in the Stanislaus River or other Central Valley rivers. It is assumed that catching fish with barbless hooks when water temperatures are below 60°F (January through May) and quickly releasing the fish causes negligible short-term stress or delays in spawning, and minimum mortality. Fishing pressure is extremely high between Goodwin Dam and Goodwin Canyon during weekends and repeated catch-and-release may stress spawning fish in the few areas of the canyon accessible to anglers. Moreover, many anglers are cited for not using barbless hooks. On the other hand, most of Goodwin Canyon and the reach between Knights Ferry and the Orange Blossom Bridge is infrequently fished, presumably no more than one to two parties per day, except on opening day when fishing pressure can be intense.

Poaching and Steelhead Adult Upstream Migration. Poaching and illegal fishing methods are believed by many to be major problems for steelhead in the lower Stanislaus River. However, no information is currently available regarding the extent of poaching and the magnitude of steelhead adult migrant loss due to poaching can not be estimated at this time.

As mentioned previously, due to budget and staff constraints, CDFG wardens infrequently patrol the river from Goodwin Dam to the Orange Blossom Bridge due to budget and staff constraints, and poaching of adult steelhead and salmon has been increasing during the last five years. Most enforcement of the fishing regulations results from sport fisherman reporting violations to the CDFG wardens using the Cal Tip hotline (Tony Spada, personal communication, 2002). However, poaching and other violations are virtually unchecked between October 16 to December 31 when the river is closed to fishing and sport anglers are not present on the river.

64


Moreover, regulations allowing bait fishing downstream of the Highway 120 Bridge is a frequent excuse for illegally using bait upstream of this section. These problems might be remedied by (1) providing funding to increase the patrol of game wardens on the river, especially from October 16 to December 31, when the river is closed to fishing, and (2) implementing new regulations requiring a catch-and-release fishery with artificial lures and barbless hooks from Goodwin dam to the mouth of the San Joaquin River.

2.3.4 Steelhead Spawning and Spawning Habitat

Steelhead Spawning and Spawning Habitat Requirements

Similar to Chinook salmon, steelhead dig a redd (nest) and deposit their eggs within the stream sediment where incubation, hatching, and subsequent emergence take place. In general, steelhead spawn in cool, clear streams featuring suitable gravel size, depth, and current velocity. Intermittent streams may be used for spawning (Barnhart 1986; Everest 1973). Gravels of 1.3 cm to 11.7 cm in diameter (Reiser and Bjornn 1979) and flows of approximately 40-90 cm/second (Smith 1973) are generally preferred by steelhead. Reiser and Bjornn (1979) reported that steelhead prefer a water depth of 24 cm or more for spawning. According to McEwan and Jackson (1996), the preferred temperatures for spawning are estimated to range between 39 F and 52 F.

Existing Stanislaus River Conditions and Effects on Steelhead Spawning and Spawning Habitat

Similar to Chinook salmon, there appear to be several factors that may influence steelhead spawning and spawning habitat in the Stanislaus River including limited spawning gravel supplies; substrate armoring and embeddedness; and increased turbidity levels. Spawning habitat has been altered as a result of reduced gravel recruitment due to gravel mining and blockage of sediments and reduced sediment transport flows caused by dams, and changes in streamside land use. Adult steelhead require covered holding and feeding habitat that is adjacent to suitable spawning habitat. Since these habitat features are relatively rare in the lower river due to in-river gravel mining and scouring of gravel from riffles in Goodwin Canyon, steelhead adults may experience insufficient spawning conditions.

Steelhead Spawning Habitat Distribution. Steelhead spawning distributions have not been extensively studied because steelhead spawning typically occurs during high, turbid flow events when observations are difficult to impossible to make. Although surveys have not been conducted to determine where steelhead spawn in the Stanislaus River, it is presumed that a majority of spawning occurs between Goodwin Dam and the Orange Blossom Bridge because that is where most adults are captured during hook-and-line fishing. Potential spawning sites that contain holding and feeding habitat, as well as spawning-sized gravel, where large adults are frequently caught include four gravel addition sites in Goodwin Canyon; seven of the KFGRP sites near Lovers Leap, Horseshoe Road, and Honolulu Bar (riffles R13, R14A, R15, R19, R19A, R28A, and R29); and four riffles adjacent to deep mine pits near Frymire Ranch, Willms Pond, and Button Bush Park.

Steelhead Preferred Spawning Areas. Hook-and-line catch of adult steelhead and rainbow trout at the KFGRP restoration riffles between Two-Mile Bar and the Orange Blossom Bridge suggests that these fish may prefer spawning sites with deep water nearby (> 4 feet) and cover

65


that is provided by either surface turbulence or large woody debris (Walser, personal communication, x). The KFGRP sites where adult rainbow trout/steelhead catch rates are relatively high include riffles R13, R14A, R15, R19, and R19A, R28A, and R29. In contrast, catch rates are low at other nearby riffles R12A, R12B, R14, and R15, which lack surface turbulence or large woody debris.

Armoring and Embeddedness and Turbidity and Steelhead Spawning. Although steelhead spawning requirements are slightly different than Chinook salmon, they are similar enough to assume that effects of existing conditions on steelhead spawning and spawning habitat are comparable to those identified for fall-run Chinook (See Section 2.1.4, Armoring and Embeddedness and Fall-run Chinook Spawning; and Turbidity and Fall-run Chinook Spawning).

2.3.5 Steelhead Incubation and Emergence

Steelhead Incubation and Emergence Requirements

Length of time required for eggs to develop and hatch is dependant on water temperature and is quite variable; hatching varies from about 19 days at an average temperature of 60F to about 80 days at an average of 42F. The optimum temperature range for steelhead egg incubation is estimated to be 46F to 52F based on various studies (Reiser and Bjornn 1979, Bovee 1978, Bell 1986, Leidy and Li 1987). Egg mortality may begin at temperatures above 56F (McEwan and Jackson 1996). The survival of embryos is reduced by 50% when fines of less than 6.4 mm comprise 30% of the substrate (Kondolf 2000). Studies have shown survival of embryos improves when intragravel velocities exceed 20 cm/hour (Phillips and Campbell 1961, Coble 1961).

Existing Stanislaus River Conditions and Effects on Steelhead Incubation and Emergence

Incubation habitat is affected indirectly by changes in streamside land use. Based on several environmental studies identified below, the primary factor that may influence fall-run Chinook egg incubation and incubation habitat in the Stanislaus River is high concentrations of fines within spawning gravels that result in low DO levels. Streamflow may also be an influencing factor. On the other hand, water temperatures appear to be suitable for steelhead incubation.

Fines, Dissolved Oxygen, and Streamflow and Steelhead Incubation and Emergence. Although steelhead incubation requirements are slightly different than Chinook salmon, they are similar enough to assume that effects of existing conditions on steelhead incubation and emergence are comparable to those identified for fall-run Chinook (See Section 2.1.5, Fines and Dissolved Oxygen and Fall-run Chinook Incubation and Emergence; and Streamflow and Fall-run Chinook Incubation and Emergence).

Water Temperature and Steelhead Incubation and Emergence. Thermograph data collected since 1998 during the steelhead incubation and emergence period indicates that maximum average daily water temperatures did not exceed 55°F to Knight’s Ferry (Figure 22) which is below the temperature where mortality begins (i.e., 56°F). Temperatures at Oakdale were also below 56°F during most of the incubation period but were between 56°F and 65°F during parts of March through June. These warmer temperatures may lead to declines in survival for any eggs or alevins incubating during these months at or below Oakdale. Since most spawning is

66


When?


anticipated to occur above OBB, a majority of incubating steelhead are likely to experience suitable temperatures throughout the entire incubation period.

2.3.6 Steelhead Juvenile Rearing

Steelhead Juvenile Rearing Requirements

The majority of steelhead in their first year of life occupy riffles, although some larger fish inhabit pools or deeper runs. Juvenile steelhead feed on a wide variety of aquatic and terrestrial insects, and emerging fry are sometimes preyed upon by older juveniles. Water temperatures influence the growth rate, population density, swimming ability, ability to capture and metabolize food, and ability to withstand disease of these rearing juveniles. Rearing steelhead juveniles have been observed to prefer water temperatures of 45° F to 60° F (Figure 22; Reiser and Bjornn 1979, Bovee 1978, Bell 1986). Temperatures above 60 F have been found to induce varying degrees of chronic stress and associated physiological responses in juvenile steelhead (Leidy and Li 1987).

Existing Stanislaus River Conditions and Effects on Steelhead Juvenile Rearing

Changes in land use, the frequency and magnitude of natural disturbances, and the development of water, hydroelectric and flood control projects are presumed to have impacts on steelhead juveniles similar to those on fall-run Chinook juveniles (see Section 2.1.6, Existing Stanislaus River Conditions and Effects on Fall-run Chinook Juvenile Rearing). However, the magnitude of impacts may be higher for steelhead because steelhead juveniles are found within the river year-round instead of only several months like fall-run Chinook which increases the chances that steelhead will be exposed to adverse conditions.

Distribution of Steelhead Juvenile Rearing. During 2000 and 2001, young rainbow trout/steelhead were observed in the Stanislaus River beginning in April as they began emerging from the gravel and were abundant from May through September (Fisheries Foundation 2002). They were found to be most abundant at the uppermost study sites in Goodwin Canyon and at Two-Mile Bar, and least abundant at Oakdale, the lowermost study site. Rainbow trout/steelhead parr were observed as far downstream as Honolulu Bar by June where they remained common throughout the summer and fall. Few were observed at Oakdale where summer water temperature was the highest, ranging between 64.4°F and 68°F.

Yearling and older trout were found to be primarily concentrated in the upper river in Goodwin Canyon and at Two-Mile Bar for most of the 2000 and 2001 surveys (Fisheries Foundation 2002). A greater density of fish were observed at the KFGRP sites at Knight’s Ferry, Lovers Leap, and the Orange Blossom Bridge than at other sites below Two Mile Bar. Abundance in Goodwin Canyon and at Two-Mile Bar appeared to increase over the summer, which may indicate a positive upstream movement of yearling trout to cooler water conditions existing closer to Goodwin Dam. In contrast, more yearling rainbow trout were observed in the downstream reaches in 2001 than 2000, although flows were lower and water temperatures were higher in 2001 than in 2000.

Young-of-the-year and Age 1+ rainbow trout/steelhead were generally equally abundant in slow and fast water in some reaches, but showed a preference for faster water in upstream reaches and

67


slower water in downstream reaches (Fisheries Foundation 2002). Both showed a strong preference for the KFGRP sites. Juvenile trout often selected flooded vegetation as it provided velocity refuge, overhead cover, and protection from predators.

Streamflow and Steelhead Juvenile Rearing. Potential influences of streamflow on juvenile rearing are likely to be similar to those identified for fall-run Chinook juvenile rearing (see Section 2.1.6, Streamflow and Fall-run Chinook Juvenile Rearing).

Water Temperature and Steelhead Juvenile Rearing. Adherence to water quality standards for temperature and DO within the Stanislaus River and Delta ensure that water temperatures in the Stanislaus River are maintained within a suitable range for juvenile steelhead rearing from December through May. On average, maximum daily water temperatures are between 50o F and 60o F in most of the river from December through May and in the reach above Knights Ferry year-round (Figure 10). Temperatures below Oakdale become near or just above stressful levels of 65°F during most of the summer. During snorkel surveys, few juveniles were observed as far downstream as Oakdale during the summer where water temperature was the highest ranging between 64.4°F and 68°F.

As mentioned previously (see Section 2.2.4 Water Temperature and Spring-run Chinook Adult Holding), USBR’s Stanislaus River Basin Water Temperature Model (Rowell 1993) predicts that temperatures below 65°F can be provided between Goodwin Dam and OBB during the summer for juvenile steelhead rearing in most years. Therefore, NOAA Fisheries has provided a term and condition in a Biological Opinion (NOAA Fisheries 2002), which states that USBR shall, to the extent possible, control water temperatures by flow releases to the lower river between Goodwin Dam and Orange Blossom Road Bridge (USGS Gauge) during June 1 through November 30, to a daily average temperature of less than or equal to 65°F to protect over-summering steelhead from thermal stress and from warm water predator species. If temperature releases are required to maintain this target, USBR, must coordinate with CDFG and USFWS to use fishery release water consistent with NMIPO, D-1641, and CVPIA. As long as this requirement is maintained, water temperatures in the primary rearing reach of the Stanislaus River will likely provide suitable year-round habitat for juvenile steelhead.

Dissolved Oxygen, Predation, Disease, Contaminants, and Unscreened Diversions and Steelhead Juvenile Rearing. Potential influences of dissolved oxygen, predation, disease, contaminants, and unscreened diversions on juvenile steelhead rearing are likely to be similar to those identified for fall-run Chinook juvenile rearing (see Section 2.1.6, Dissolved Oxygen and Fall-run Chinook Salmon Juvenile Rearing; Predation and Fall-run Chinook Salmon Juvenile Rearing; Disease and Fall-run Chinook Salmon Juvenile Rearing; Contaminants and Fall-run Chinook Salmon Juvenile Rearing; and Unscreened Diversions and Fall-run Chinook Juvenile Rearing).

Food Availability and Steelhead Juvenile Rearing. Although no invertebrate studies have been reported for the lower Stanislaus River in order to determine whether food availability is a limiting factor within the Stanislaus River, an analysis of the length/weight relationship of rainbow trout/steelhead juvenile was conducted which can provide an indirect indication of food availability. Analysis of rainbow trout/steelhead length and weight data from individuals greater than 200 mm that were captured in the rotary screw trap at Oakdale indicates that their relative weight, a type of condition factor, is above average with regard to typical management standards.

68


Relative weight is expressed as a percentage where 100% represents a better-than-average condition factor to which fish managers might aspire (Murphy and others 1991). Average relative weights in the literature generally range between 85% and 95% for most fish species. The condition factor calculated for O. mykiss captured in the Stanislaus River at Oakdale between 1996 and 2002 was 100.2%. Based on this relatively high condition factor, it appears that food availability for rainbow trout/steelhead is adequate.

2.3.7 Steelhead Juvenile Migration

Juvenile Steelhead Migration Requirements

The optimal thermal range during smoltification and seaward migration for steelhead has been estimated to be 44 F to 52 F based on various studies (Leidy and Li 1987, Rich 1997) and temperatures above 55.4 F have been observed to inhibit formation and decrease activity of gill (Na+ and K+) ATPase activity in steelhead, with concomitant reductions in migratory behavior and seawater survival (Zaugg and Wagner 1973, Adams et. al 1975).

Existing Stanislaus River Conditions and Effects on Juvenile Steelhead Migration

Based on results from fishery and environmental analyses, there appear to be two primary factors that may influence juvenile steelhead migration including streamflow and water temperature. In addition, predation may be an influencing factor, particularly during dry years.

Streamflow and Juvenile Steelhead Migration. Steelhead smolt survival in the San Joaquin basin may be dependent on springtime flows. Although smolt survival studies have not been conducted for steelhead in the San Joaquin basin, an indirect measure of smolt survival can be obtained by comparing the number of adult steelhead caught by anglers with the abundance of fall-run Chinook salmon returning to the river and the magnitude of flows during smolt outmigration. The number of adult steelhead captured by anglers has followed the same pattern observed for fall-run Chinook salmon escapement in the San Joaquin basin: namely that catch and escapement substantially increase two years following flood flows. Mr. Steve Walser (personal communication, X) reported that his catch of adult steelhead, with hook-and-line greatly increased in all three San Joaquin River tributaries including the Stanislaus River in 1997, 1999, 2000, and 2001. In 1997, adult steelhead captured were between 12-15 inches in length and weighed about one-half pound, while in 1999 through 2001, they were larger and weighed from 2 to 13 pounds.

The increased catch rate of adults in 1997 may be the result of unusually high flows in the San Joaquin Delta during 1995 (20,000 to 25,000 cfs at Vernalis between March and June) with associated increases in smolt survival (assuming that adults return from the ocean two years later; it should be noted that approximately 57% of Sacramento River steelhead spawn after 1 year in the ocean, and approximately 43% spawn after 2 years in the ocean (Busby and others 1996). Likewise, the unusually high springtime flows that occurred in the San Joaquin Delta in 1997 (Vernalis flows exceeded 25,000 cfs between January and March) and 1998 (Vernalis flows ranged between 15,000 and 35,000 cfs between mid February and June) could have increased smolt survival which would explain the relatively large adults caught from 1999 through 2001. Between 1992 and 1997, most trout caught were between 10 and 12 inches in length with a few larger fish up to 13 pounds. During this time, a minimum flow of 200 cfs was

69


When?


maintained in the Stanislaus River which likely provided suitable spawning and rearing habitat for steelhead, but may have resulted in lower survival for migrating smolts as compared to survival rates under higher flows from 1995 through 1999.

It is not likely that instead of increasing survival of smolting fish, high flows could simply have attracted larger adult steelhead from the Sacramento River basin. If this was the case, then catch rates of large steelhead should have been higher in 1995, 1997, and 1998 (when Vernalis flows were high) than they were in 1999 and 2000 (when Vernalis flows ranged between 10,000 and 17,000 cfs for about a month in February and March).

Water Temperature and Juvenile Steelhead Migration. Juvenile steelhead smolts have been captured in rotary screw traps in the Stanislaus River throughout the sampling period from December through July, with no apparent peak in migration timing. It is unknown whether smolts also migrate during other times of the year due to lack of sampling in other months. Average daily water temperatures in the Stanislaus River are suitable for smolting (i.e., 44°F to 52°F) between November and February in the entire river (Figure 10) indicating conditions are sufficient for smoltification. Temperatures in the lower river below Oakdale can be above 60°F from mid-June to October which may act as a migration impediment for any juvenile steelhead migrating through the lower river during this time. Under such conditions fish may residualize and emigrate as yearlings the following spring.

Dissolved Oxygen, Predation, Disease, Contaminants, and Unscreened Diversions and Steelhead Juvenile Migration. Potential influences of dissolved oxygen, predation, disease, contaminants, and unscreened diversions on juvenile steelhead migration are likely to be similar to those identified for fall-run Chinook juvenile rearing (see Section 2.1.6, Dissolved Oxygen and Fall-run Chinook Salmon Juvenile Rearing; Predation and Fall-run Chinook Salmon Juvenile Rearing; Disease and Fall-run Chinook Salmon Juvenile Rearing; Contaminants and Fall-run Chinook Salmon Juvenile Rearing; and Unscreened Diversions and Fall-run Chinook Juvenile Rearing).

3 SUMMARY OF INFORMATION FOR STANISLAUS RIVER SALMONID POPULATIONS OUTSIDE OF THE STANISLAUS RIVER (I.E., DELTA AND OCEAN)

3.1 ADULT CHINOOK SALMON AND STEELHEAD IN THE DELTA

3.1.2 Adult Chinook Salmon and Steelhead Migration through the Delta

Chinook Salmon and Steelhead Adult Upstream Migration Requirements

70


Adult migration requirements for salmonids include suitable temperatures to maintain egg viability (i.e., less than 65°F), suitable DO levels (i.e., ≥5 mg/L), and adequate passage to the spawning grounds (i.e., no physical or hydraulic barriers/impediments). Unusual water temperatures or DO levels during upstream migration periods can alter or delay migration timing, accelerate or retard mutations, and increase fish susceptibility to diseases.

Peak fall-run adult migration typically occurs during October. Spring-run migration from the ocean into the Delta can begin as early as January (CDFG 1998c) and extend through July (Myers and others 1998). Adult steelhead migrate upstream in the Sacramento River mainstem from July through March, with peaks in September and February (Bailey 1954; Hallock and others 1961).

Existing Delta Conditions and Effects on Chinook Salmon and Steelhead Adult Upstream Migration

Based on radio-tagging and CWT studies, the primary factors that may influence Chinook salmon and steelhead adult upstream migration in the Delta are changes in hydraulic conditions within the Delta as a result of export operations, low DO near Stockton, high water temperatures, or a combination of these factors.

Delta Flow Conditions and Chinook Salmon and Steelhead Adult Upstream Migration. Potential straying problems may occur due to changes in hydraulic conditions within the Delta as a result of export operations. Straying is the term used to indicate when a migrating salmon does not return to their natal (“home”) stream or stream reach (Quinn 1993). From an evolutionary standpoint, straying provides the opportunity to colonize new habitats (Milner and Bailey 1989) and promotes genetic heterogeneity at the population level (Utter and others 1989). However, on an individual basis, returning to a natal stream is more likely to lead to successful spawning because the fish can “predict” that there will be good quality spawning and rearing habitat in their natal stream (habitat within the stream supported the fish when it was rearing) compared to the gamble associated with straying to an unknown stream with unknown habitat quality.

CVP and SWP diversion of water at times can cause net reverse flows in the lower San Joaquin River which brings Sacramento River water into its channels. The mixture of water from both systems in the interior Delta channels may confuse returning adult spawners bound for either the San Joaquin or Sacramento River basins, resulting in delays and straying. In particular, those fish trying to return to the Sacramento River system can experience detours towards Georgiana Slough and the Delta Cross Channel, with the possibility of ending up in the Mokelumne River (Chadwick 1982; SSR 2001).

Between 1964 and 1967, Hallock and others (1970) conducted a radio-tagging study to characterize migration patterns of adult fall-run Chinook salmon within the Delta. During this study, they documented that the rate of straying to non-natal rivers was highly correlated with the percentage of San Joaquin River flow that was exported at the SWP and CVP delta pumping facilities.

In addition to Hallock and others’ (1970) study, an analysis of coded-wire tagged (CWT) data from returning San Joaquin basin fall-run Chinook salmon adult spawners (Mesick 2001b) between 1979 and 1996 corroborates that straying is correlated with the percentage of San

71


Joaquin River flow exported at the SWP and CVP delta pumping facilities (Figure 23). This CWT analysis determined that the percentage of hatchery CWT San Joaquin basin fall-run salmon that strayed increased from a rate of less than 3% (export rates below 300% of San Joaquin flows at Vernalis) to about 17% (export rates above 400% of San Joaquin flows at Vernalis). These straying rates are indicative of rates for hatchery salmon reared in the Merced River hatchery and subsequently released at other locations within the San Joaquin Basin. Other studies have shown that hatchery fish reared in one stream and released in another have increased straying rates compared to those released within their rearing stream (Hallock and Reisenbichler, 1979; Dettman and Kelley, 1987; Cramer 1990), therefore, the straying rates based on Merced River CWT data may not reflect the straying rates of fish “naturally” spawned and reared within the Stanislaus River.

While straying rates of natural fall-run Chinook adults may be different than those analyzed, it is reasonable to expect that whenever high exports occur in conjunction with low San Joaquin River flows that little, if any, San Joaquin River water reaches the San Francisco Bay, and, as a result, there is the potential for increased straying rates due to limited olfactory cues which are necessary to guide salmon back to their natal stream (Mesick 2001b). No adult migration studies have been conducted within the Delta specifically for spring-run or steelhead, however, it is likely that adult spring-run and steelhead would behave similarly in response to Delta hydraulic conditions and may experience increased straying rates when exports are greater than 400% of San Joaquin River flows at Vernalis. Exports greater than 400% would likely be a greater problem for increased straying during peak adult migration periods which typically occur in October (fall-run); May through July (spring-run); and September and February4 (steelhead).

4 Peak steelhead adult migration timing is unknown in the San Joaquin River, however, peaks observed in the Sacramento River include September and February.

72


5%

10%

15%

20%

Perc

ent S

tray

s of

Mer

ced

Hat

cher

y Fi

sh

0 2 4 6 8Average Export/Flow Ratio 15 to 21 Oct

83 84

85

86

87

88 89

9092

9394

95

96

Straying Rates and Delta Exports

Figure 23. Estimated percent of adult CWT Chinook salmon that were reared at the Merced River Hatchery, released in the San Joaquin basin as juvenile salmon, and subsequently strayed to the Sacramento River and eastside tributary basins to spawn relative to the average ratio of Delta export rates at the CVP and SWP pumping facilities to San Joaquin River flow rates at Vernalis between October 15 and 21, 1983 to 1996.

Based on the recognition that increased straying can occur at high export percentages, pulse flows released from the San Joaquin tributaries and/or reductions in Delta exports for 10 days in mid-October since 1993 have kept Delta export rates to less than 300% of the San Joaquin River flow at Vernalis during the typical peak of fall-run upstream migration (Figure 24). Therefore, straying rates were probably less than 3% between 1993 and 2002.

Export rates have exceeded 400% of San Joaquin River flows at Vernalis between November and April during dry years (e.g., 1990, 1991, 1992, and 2002) and in July during most years between 1990 and 2002 (Figure 25). Therefore, it is possible that high rates of Delta exports in dry years during migration periods may cause adult spring-run and/or steelhead attempting to migrate to the Sacramento River to stray into the San Joaquin Basin with straying rates up to 17% similar to fall-run Chinook. In addition, high export rates during July of all years may result in similar straying opportunities.

73


0%

50%

100%

150%

200%

250%

300%M

ean

Del

ta E

xpor

ts/V

erna

lis F

low

s

1993 1994 1995 1996 1997 1998 1999 2000 2001 2002

Figure 24. The ratio of combined exports at the CVP and SWP facilities during a 10-day pulse flow period in mid-October from 1993 to 2002.

74


0%

200%

400%

600%

800%

1000%M

ean

Del

ta E

xpor

ts/V

erna

lis F

low

s

Feb Mar Apr May Jun Jul

90 91 92 93 94 95 96

97 98 99 00 01 02

Figure 25. Mean monthly percentage of San Joaquin River flow at Vernalis that was exported at the State Water Project and the Federal Water Project during February through March from 1990 to 2002. Data collected during wet years and above normal years are indicated with hourglass and oval symbols, respectively.

Dissolved Oxygen and Water Temperature, and Chinook Salmon and Steelhead Adult Upstream Migration. Between 1964 and 1967, Hallock and others (1970) determined that migration of radio-tagged adult fall-run Chinook salmon was delayed at Stockton whenever DO concentrations were less than about 5 mg/l (4.5 mg/L in 1967 and 5.5 mg/L in 1965) and/or water temperatures exceeded about 65°F in October. Hallock and others (1970) could not distinguish between the impacts of high water temperature and low DO concentrations and it is possible that the observed delays resulted from the effects of both DO and temperature. Migration delays of adult salmon in the deep-water ship channel near Stockton may reduce gamete viability particularly if the fish are exposed to high temperatures for prolonged periods. CDFG reported that the quality and survival of eggs was poor from females exposed to water temperatures that exceeded 56°F (CDFG 1992), which is similar to the findings of other studies.

Although no studies have been conducted specifically for spring-run or steelhead, it is reasonable to assume that unsuitable water quality in the deep-water ship channel would result in similar migration delays for adult spring-run and steelhead. Based on DO levels measured near Stockton (DWR’s Burns Cut Off Road gaging station), fall-run and spring-run Chinook salmon and steelhead may experience migration delays in the lower San Joaquin River during all or part of their upstream migration when DO is below 5 mg/L (Figure 26 and Figure 27). Low DO in the

75


deep-water ship channel near Stockton could potentially delay the upstream migration of adult salmonids for extended periods during dry years and for brief periods during normal water years. Once adults pass Stockton, it is unlikely that they encounter low DO conditions that would cause any further delays.

0

2

4

6

8

10

Min

imum

Diss

olve

d O

xyge

n (p

pm)

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

90 91 92 93 94 95 96

97 98 99 00 01 02

Figure 26. Minimum DO concentrations measured at hourly intervals at the Department of Water Resources’ Burns Cut Off Road monitoring station during the adult spring-run Chinook salmon migration period from 1990 to 2002. Data collected during wet years and above normal years are indicated with hourglass and oval symbols, respectively.

DO levels consistently exceeded 5 mg/L near Stockton during all or part of October (fall-run Chinook migration) between 1983 and 1990, while in 1991 and 1992 under drought conditions, DO remained below 5 mg/l for most of October. In fall 1992, the Head of Old River Barrier was installed but it did not result in increased DO levels above 5 mg/l until late October (Figure Figure 27). In 1993, DO levels were low until about October 10 and it is likely that pulse flows that raised Vernalis flows to about 4,000 cfs on October 7 were responsible for increasing DO levels. Similarly in 1994, DO levels were low until October 15 when pulse flows raised Vernalis flows to about 2,000 cfs. In 1995, DO levels were at least 6 mg/L in October when Vernalis flows ranged from about 3,000 cfs to 6,000 cfs through mid-October. DO levels in 1996 were low or fluctuated greatly until October 13 when pulse flow releases increased Vernalis flows from 2,000 to about 3,000 cfs.

76


The minimum DO recorded near Stockton was periodically below 5 mg/L throughout the spring-run migration period from 1990 to 2002 (Figure 27). The lowest measurements were recorded in 1992 and 2002 which were relatively dry water years. In 1992, the DO was continuously below 5 mg/L between late-February and mid-April and it fluctuated near 5 mg/L between mid-May and the end of July (Figure 27). In 2002, the DO fluctuated near 5 mg/L between February 15 and March 6 and fluctuated again near or below 5 mg/L between June 15 and July 31. The DO fluctuated near 5 mg/L between mid-June and the end of July during most years except 1995 and 1998.

0

2

4

6

8

10

12

Dis

solv

ed O

xy

gen

(p

pm

)

Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec1992 2002

Figure 27. Hourly dissolved oxygen measurements at the Department of Water Resources’ Burns Cut Off Road monitoring station in 1992 and 2002.

DO concentrations in the San Joaquin River near Burns Cut Off Road in the deep-water ship channel near Stockton were periodically below 5 mg/L during the adult steelhead migration period, particularly during October and June. Few adult steelhead are caught in October and June in the lower Stanislaus River (Walser, personal communication, X), however, it is unknown whether the low numbers observed during these months are due to natural migratory behavior or are due to unfavorable migratory conditions (e.g., low DO) in the deep-water ship channel. During the peak migratory period for steelhead (September and February4), DO was lower than 5 mg/L. In 1992, the DO was continuously below 5 mg/L between late-February and mid-April. In 2002, the DO fluctuated near 5 mg/L between mid-January and March 6.

77


When?


The water temperature in the San Joaquin River near Stockton may cause adult spring-run Chinook salmon to delay their upstream migration since mean monthly water temperatures (calculated from hourly data provided at DWR gaging station), exceeded 65°F during April in dry years and during June in all water year types between 1990 and 2002 (Figure 28). However, as previously mentioned (see Section 2.1.3, Fall-run Chinook Adult Upstream Migration Requirements) thermal tolerances and blockage temperatures identified in past studies do not appear to reflect fish survival and behavior observed under “natural” field conditions in the Central Valley. Recent observations of adult salmon passage during a Stanislaus River weir monitoring study in 2003 indicate that salmon had to migrate for prolonged periods at average daily water temperatures above 70°F (Figure 6) in the Delta and lower San Joaquin to reach the weir site. These observations indicate that spring-run migration may occur at higher temperatures than previously thought, particularly when DO is levels are high.

The mean water temperature in the deep-water ship channel probably does not cause adult steelhead to delay their upstream migration, except in October. Between 1990 and 2002, the mean monthly water temperatures, derived from hourly recordings at the DWR Burns Cut Off monitoring station, exceeded 65°F in October in most years (Figure 28).

Figure 28. Mean monthly water temperature measured at hourly intervals at the Department of Water Resources’ Burns Cut Off Road monitoring station from 1990 to 2002. Data collected during wet years and above normal years are indicated with hourglass and oval symbols, respectively.

DO and temperature conditions that delay adult salmon migration may not cause increased rates of straying based on data presented in Hallock and others (1970). Only 15% of Hallock’s tagged

45

50

55

60

65

70

75

80

85

Mea

n W

ater

Tem

per

atu

re (

F)

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

90 91 92 93 94 95 96

97 98 99 00 01 02

78


study fish strayed in 1965 and 1967, when DO was less than 5.5 mg/L in mid-October and many fish were delayed at Stockton. Conversely, 54% of the study fish strayed in 1964 when DO exceeded 5.5 mg/L in mid-October and few fish were delayed.

In summary, the combined effects of low DO and high water temperature could delay the upstream migration of adult salmonids during all, or portions, of their migration period depending on water year type. In contrast, spring pulse flow releases made from the San Joaquin tributaries between April 15 and May 15 since 1998 to enhance the survival of fall-run juveniles emigrating to the Delta/ocean have likely improved conditions for adult spring-run and steelhead to migrate upstream through the deep-water ship channel near Stockton.

Passage and Chinook Salmon and Steelhead Adult Upstream Migration. In the South Delta, rock barriers are installed from spring through fall to maintain hydraulic head for small pump diversions and these barriers are impassible by adult salmonids. Hallock and others (1970) conducted a radio tracking study between 1964 and 1967 to determine migration routes and travel time for fall-run Chinook salmon between the Delta and the tributaries. During their investigations, they found that when a rock barrier was installed at the head of Old River (a tributary to the San Joaquin River) in fall 1964, adult salmon traveling to spawning sites within the San Joaquin Basin migrated upstream through the mainstem San Joaquin River. However, when the barrier was not installed in fall 1965 through 1967, some salmon migrated through the South Delta to get to their San Joaquin spawning sites. This study suggests that the rock barriers reduce attraction flows to secondary channels or tributaries, so few, if any, adults would be expected to migrate into channels where rock barriers have been installed.

3.2 JUVENILE CHINOOK SALMON IN THE DELTA

3.2.2 Juvenile Chinook Rearing and Migration in the Delta

Juvenile Chinook Salmon Estuarine Rearing and Migration Requirements

Juvenile fall-run salmon may rear for up to several months within the Delta before ocean entry (Kjelson and others 1982). Rearing within the Delta occurs principally in tidal fresh water habitats. Juveniles typically do not move into brackish water until they have undergone smoltification, after which NOAA fisheries studies indicate they move quickly to the ocean (MacFarlane and Norton 2002). Rearing requirements in the Delta are similar to those discussed previously for juvenile rearing and migration in the Stanislaus River.

Existing Delta Conditions and Effects on Juvenile Chinook Salmon Rearing and Migration

Based on trawling surveys during dry water years in the late 1940s, a majority of the juvenile fall-run Chinook salmon caught in the Delta during February and March were fry from the Sacramento River basin, but during April through June/July were primarily parr and smolt-sized fish from the San Joaquin River basin (Erkkila and others 1950). However, recent screw trapping studies suggest that most of the juvenile salmon in the lower Stanislaus River begin their downstream migration as fry during all water year types (Figure 29); whereas, few fry survive their migration to the San Joaquin River during dry and normal water years (see Section 2.1.7 Streamflow and Juvenile Fall-run Chinook Migration). Juvenile migrations from the Stanislaus

79


River coincided with the onset of peak flows in 1996, 1998, 1999, and 2000 (Demko and Cramer 1997; Demko and others 1999 and 2000).

Figure 29. The estimated number of fry, parr, and smolt-sized juvenile Chinook salmon passing the screw trap at Oakdale in the lower Stanislaus River. Sampling during 1998 and 1999 began in mid February and so most, but not all fry, were probably captured during these years.

Of the juvenile Chinook salmon from the Stanislaus River that successfully migrate into the San Joaquin River and Delta to rear, few are thought to survive except during flood years. Ocean recovery rates of fry obtained from the Coleman National Fish Hatchery and tagged with coded wire half tags indicate that fry survival was lower in the Central Delta near the mouth of the Mokelumne River than in the North Delta near Courtland, Ryde, or Isleton during dry years, but the difference was not statistically significant (Brandes and McLain 2001). However, during flooding in 1982 and 1983, tagged fry survived at similar rates in the Central Delta and South Delta in the Old River compared to the North Delta (Brandes and McLain 2001). The estimated poor survival of juveniles rearing in the Delta in dry and normal water years may be caused by a variety of factors such as predation; entrainment at numerous small, unscreened diversions; unsuitable water quality; and/or direct mortality at the state and federal pumping facilities in the Delta. Entrainment at the Delta pumping facilities does not appear to occur during very wet years since tagged fry were only collected at the pumping facilities during dry years (Brandes and McLain 2001).

0

500,000

1,000,000

1,500,000

2,000,000

To

tal

Es

tim

ate

d P

as

sa

ge

1998 1999 2000 2001 2002 2003

Smolt (>/=80 mm Parr (45-79 mm) Fry (<45 mm)

Outmigrant Abundance at Oakdale

80


Delta Flow Conditions and Juvenile Chinook Salmon Rearing and Migration. The downstream migration of fall-run Chinook smolts generally begins in early April, peaks between late April and mid-May (dry years) or late May (normal and wet years), and then rapidly declines in June as determined by trawling at Mossdale (CDFG 1991 to 1998). Screw trapping at Caswell State Park in the Stanislaus River between 1996 and 1999 indicates that fall-run Chinook smolts migrate downstream and out of the river primarily between April and May with a few migrating downstream through mid-July (Demko and others 2000).

Smolt survival has been studied by the USFWS and CDFG since 1982 by releasing groups of about 25,000 to 100,000 hatchery reared juveniles with coded-wire-tags (CWT) at various locations in the tributaries and Delta in April and May and recapturing them with a trawl at Mossdale and Chipps Island to investigate the effects of flows and exports (Brandes and McLain 2001). The following discusses the results of these studies: (1) smolt survival may be lowest in the deep-water ship channel from the Port of Stockton to the mouth of the Mokelumne River, (2) smolt survival is not related to water temperature or DO concentration, and (3) installing a barrier at the head of Old River (HORB) appears to ameliorate the impacts of exports by preventing entrainment of smolts in the Old River and toward the pumping facilities and by increasing flow and DO and reducing water temperatures in the deep-water ship channel. The absolute survival estimates for juveniles migrating through the Delta in the mainstem San Joaquin River in spring 1991 were somewhat lower in the deep-water ship channel between Stockton and Jersey Point than in the upstream reach between Dos Reis and Stockton (Figure28); absolute survival indices are computed by dividing the relative survival index for the upstream site by the relative survival index for the downstream site in. Absolute survival for Feather River hatchery smolts in mid April was 72.0% between Dos Reis and Stockton (Buckley Cove) but only 17.4% between Stockton and Jersey Point based on ocean recoveries.

This computes to a mortality rate of 2.55% per mile for the 11-mile reach between Dos Reis and Stockton and a mortality rate of 3.05% per mile for the 27-mile reach between Stockton and Jersey Point. During a second test in early May 1991, no releases were made at Dos Reis but absolute survival of the Feather River smolts migrating between Stockton and Jersey Point was similarly low at 17.9%; which equates to a mortality rate of 3.04% per mile. During the April 1991 test, Vernalis flows averaged 1,150 cfs, total Delta exports averaged 4,283 cfs, DO averaged 6.3 mg/L at Rough and Ready Island near Stockton, water temperature was about 60°F near Stockton, and flows in the Delta Cross Channel and Georgiana Slough averaged about 4,000 cfs. During the May 1991 test, Vernalis flows averaged 959 cfs, total Delta exports averaged 2,613 cfs, DO averaged 5.4 mg/L at Rough and Ready Island near Stockton, water temperature was about 65°F near Stockton, and flows in the Delta Cross Channel and Georgiana Slough averaged about 3,500 cfs.

81


Figure 30. Map of Delta release and recovery locations.

Table 3. The number of tagged juvenile Chinook salmon released at the various study sites in the Delta in 1991, the number recovered in the ocean fisheries, and the survival index used to estimate absolute survival and mortality rates.

The smolt survival tests in 1991 did not provide consistent results regarding the effects of increased flows downstream of the lower Mokelumne River provided by diversions of Sacramento River water through the Delta Cross Channel and Georgiana Slough. In April 1991, absolute smolt mortality rate in the 20-mile reach between Stockton and the lower Mokelumne River was 3.0% per mile whereas it was 8.1% in the 7-mile reach with increased flows between the lower Mokelumne River and Jersey Point. In contrast during May 1991, the absolute smolt mortality rate between Stockton and the lower Mokelumne River was 3.9% per mile wheras it

Date Release Site Number Released Ocean Recoveries Survival IndexApril 1991 Dos Reis 102,999 89 0.0009April 1991 Buckley Cove 99,341 115 0.0012April 1991 L. Mokelumne 47,289 141 0.0030April 1991 Jersey Point 52,139 358 0.0069May 1991 Buckley Cove 99,820 103 0.0010May 1991 L. Mokelumne 45,706 229 0.0047May 1991 Jersey Point 49,184 275 0.0056

Delta Cross

Channel

J ersey Point

Mossdale

Dos Reis

BuckleyCove

Chipp’sIsland

Lower Mokelumne

82


was 2.3% per mile in the reach with increased flows between the lower Mokelumne River and Jersey Point. The difference between these tests is caused by differences in the number of fish recovered from the groups of test fish released at the lower Mokelumne River. Recoveries of the Stockton groups and the Jersey Point groups declined slightly for the May studies compared to the April studies as would be expected if mortalities increased due to water temperatures. However, the number of test fish recovered for the lower Mokelumne River group during May was about 60% greater than the number recovered in April even though survival should have been better for the April test. One possible explanation is that the fish released at the lower Mokelumne River site in April were in relatively poor condition (e.g., unusually small or diseased) compared to other groups.

In addition to smolt survival studies conducted in the Delta, tagged smolts were released at Port Chicago in Suisun Bay and near the Golden Gate Bridge in San Francisco Bay to estimate survival through the Bay in 1984, 1985 and 1986 (Brandes and McLain 2001). Survival estimates through the Bay ranged between 76% and 84%, which are relatively high compared to the survival estimates in the Delta.

The number of recruits-per-spawner from 1952 to 2000 is well correlated with San Joaquin River flows at Vernalis during the spring between 15 April and 15 May (Figure 31). Pearson correlation coefficients (r) and probabilities (P) for the relationships between the number of recruits-per-spawner and the mean monthly flow in the San Joaquin River at Vernalis are stronger than for those with the mean monthly releases from Goodwin Dam (Table 4). F-tests indicate that the correlations for the months from March through June are significantly stronger (P < 0.002) for Vernalis flows than for Goodwin Dam releases (Appendix 1). The correlations with Vernalis flows were strongest in March, April, May, and June. The weak and non-significant correlation between the mean Goodwin Dam releases in December and the number of recruits-per-spawner suggests that flooding has no detectable affect on incubating salmon eggs.

These analyses suggest that flow affects juvenile survival between March and June as they migrate downstream toward the Delta. It is unlikely that flood flows directly affect survival (i.e., fast moving, deep water), but rather help reduce the combined impacts from predation, high water temperatures, low DO concentrations, contaminants, and entrainment at diversions in the Stanislaus River, San Joaquin River, and Delta. It is also likely that flood flows improve food availability by inundating floodplain habitats in the lower Stanislaus River basin.

Table 4. Pearson correlation coefficients (r) and probabilities (P) for the relationships between the number of recruits-per-spawner of fall-run Chinook salmon in the Stanislaus River and flows at Vernalis and flow releases from Goodwin Dam from December through June and during the April 15 to May 15 VAMP period for 35 observations between 1952 and 2000.

83


Vernalis Goodwin Damr P R P

Dec -- -- 0.01 0.97Jan 0.23 0.19 0.21 0.22Feb 0.43 0.01 0.32 0.06Mar 0.70 0.00 0.67 0.00Apr 0.75 0.00 0.58 0.00May 0.71 0.00 0.55 0.00Jun 0.68 0.00 0.64 0.00VAMP 0.74 0.00 -- --

Maintaining a low combined rate of export at the State’s Harvey O. Banks pumping facilities (SWP) and the Federal pumping facilities at Tracy (CVP) during the April-May outmigration period beginning in 1994 may not have resulted in an increased number of recruits-per-spawner observed since 1994 (Figure 31).The number of recruits-per-spawner during 1996, 1997, 1998, 1999 and 2000 when export rates were reduced for 30 days, are relatively low. In contrast, only the 1998 and 1999 estimates were low in the plots with streamflow in the San Joaquin River at Vernalis (). This suggests that the magnitude of streamflow in the San Joaquin River and Delta is more important to juvenile survival than is the rate of pumping in the Delta.

0

5

10

15

20

25

30

Rec

ruits

/Spa

wne

r

0.01 0.1 1 10 100Exports/Vernalis Flows

53 5556

57

58

5960 61

62

65

66

67

68

69

70

71ERR

737475 7677

8283

8485

86

878889 90

9194

95

9697

98

9900

Pre 1994 Post 1994

San Joaquin River Flow and Exportsand Stanislaus River Recruitment

Figure 31. The relationship between the number of fall-run Chinook salmon recruits/spawner to the lower Stanislaus River and average ratio of combined exports at the SWP and CVP pumping facilities in the Delta

84


between 15 April and 15 May from 1952 to 2000. The estimated number of recruits/spawner assumes that recruit abundance is unaffected by spawner abundance after spawner abundance exceeds 2,000 Age 3 equivalent fish. Recruit/spawner estimates are not shown for those with spawner abundance less than 493 Age 3 equivalent fish.

Water Temperature and Juvenile Chinook Salmon Rearing and Migration. Currently, there are no flow or water temperature standards to maintain suitable habitat for juvenile salmon in the mainstem San Joaquin River below the mouth of the Stanislaus River. The relationship between streamflow at Vernalis and the daily range in water temperature at Vernalis for periods in April, May, and early June in 1962, 1963, 1970, and 1973 to 1994 suggest a flow of about 3,500 cfs from mid April to mid May is adequate to maintain maximum daily water temperatures below 65°F at Vernalis (Appendix 3). Usually, adequate water temperatures occurred in the San Joaquin River except during drought years (1977 and 1987 to 1992), and when high flows entered the San Joaquin River from the James Bypass upstream of Newman during spring 1986. By the end of May, water temperatures range between 65°F and 70°F regardless of flow between 3,000 cfs and 30,000 cfs.

Recent studies of Merced River hatchery fish migrating from Mossdale with the head of the Old River barrier installed or Dos Reis without the barrier to Jersey Point suggest that survival is not correlated with water temperature (Figure 32) or DO concentration (Figure 33) in the deep-water ship channel near Stockton (SJRGA 2002 and 2003). The absolute survival estimates are based on the ocean catch for studies between 1996 and 1999 and the Chipps Island trawls estimates for 2000 and 2001, estimated flow near Stockton, and mean daily water temperature in the Stockton ship channel near Burns Cutoff Road during a 10-day period after the study fish were released.

0%

10%

20%

30%

40%

50%

60%

Abs

olut

e Sm

olt S

urvi

val

62 64 66 68 70 72Water Temperature (F)

96

9798

99

00

00

00

01

01

0101

02

02

0202

85


Figure 32. The absolute survival of CWT juvenile salmon from the Merced River Hatchery released at Mossdale with the HORB installed or at Dos Reis in April or early May from 1996 to 2002 relative to the mean daily water temperature in the Stockton ship channel near Burns Cutoff Road.

0%

10%

20%

30%

40%

50%

60%

Abs

olut

e Sm

olt S

urvi

val

7.8 8 8.2 8.4 8.6 8.8 9 9.2 9.4 9.6Dissolved Oxygen (ppm)

96

9798

99

00

00

00

01

01

01 01

02

02

0202

Figure 33. The absolute survival of CWT juvenile salmon from the Merced River Hatchery released at Mossdale with the HORB installed or at Dos Reis in April or early May from 1996 to 2002 relative to the mean DO concentration in the Stockton ship channel near Burns Cutoff Road.

Net pen studies at the release points indicated that most (>95%) of the test fish survived for 48 hours during the 2000 and 2001 studies although water temperatures ranged between 68°F and 72°F during the second release tests (May 7 and 8) at the Durham Ferry, Mossdale, and Jersey Point test sites (SJRGA 2001, 2002, 2003). These tests suggest that either mortality occurred more than 48 hours after release and/or other factors, such as predation, contributed to the mortalities.

Predation and Juvenile Chinook Salmon Rearing and Migration. Striped bass, Sacramento pikeminnow, and largemouth bass are predators of juvenile salmon in some Delta habitats. Pickard and others (1982) reported that juvenile salmon predation was high for both Sacramento pikeminnow and striped bass in the Sacramento River Delta between 1976 and 1978. They used gill nets set in Horseshoe Bend and near Hood to collect predators between February 1976 and February 1978. The results suggest that 150 to 1,050 mm fork length striped bass and 300 to 700 mm fork length Sacramento pikeminnow primarily fed on fry and relatively few smolts as

86


feeding rates were highest in winter (Dec-Feb), when 77.7% had fish in their stomachs, and low during the spring (Mar-May), when only 23.3% had fish in their stomachs. However, gastric evacuation rates are affected by several factors, including predator and prey species, predator size, size and type of meal, and water temperature so an in depth analysis is needed to determine the relative predation rates for fry and smolts by predator species. Relatively few steelhead, white catfish (Ictalurus catus), channel catfish (I. punctatus), and black crappie (Pomoxis nigromaculatus) were caught in the gill nets at Horseshoe Bend.

Nobriga and others (2003) used seines and experimental gillnets to sample Age 0 and Age 1+ striped bass and largemouth bass in 3 to 13-foot-deep water in the Yolo-Bypass, lower Sacramento River, and in the Central Delta from March through June 2001. They reported that only 1 juvenile Chinook salmon was found in the stomachs of 81 striped bass and another juvenile Chinook salmon was found in the stomachs of 63 largemouth bass, indicating that bass have less of an impact on migrating smolts during the spring than do Sacramento pikeminnow. These predators were primarily feeding on yellowfin goby (Acanthogobius flavimanus), gammarid amphipods, Corophium, and/or aquatic insects. The density of Chinook salmon during the study period was not described, and if low during the time of the study, may explain low predation rates.

Densities of black bass and striped bass are about three times higher in the central Delta downstream from Rough and Ready Island near Stockton and in the Mokelumne River (eastern Delta) than in the northern or southern areas of the Delta based on the CDFG resident fish study conducted from 1980 to 1983 (Table 4, CDFG, unpublished data). CDFG introduced Florida largemouth bass into the Delta in the early 1980s and again in 1989 and catch rates of black bass have increased since 1993 (Lee 2000). Although predation of juvenile salmon in the Delta has not been quantified, it would account for the low survival rates of juvenile salmon migrating between Dos Reis and Jersey Point and for Sacramento River juveniles migrating into the Mokelumne River through the Delta Cross Channel.

Table 5. Number and mean fork length of largemouth bass, smallmouth bass, and striped bass per kilometer that were collected during CDFG electrofishing surveys in the Sacramento-San Joaquin Delta, 1980 to 1983. The sampling sites in each region of the Delta are shown in Figure 1 of Schaffter (2000).

Location Largemouth Bass208 mm FL

Smallmouth Bass225 mm FL

Striped Bass140 mm FL

Central Delta 12.81 0.02 0.03Eastern Delta 12.92 0.20 0.19Southern Delta 4.42 0.36 0.03Northern Delta 3.83 0.78 0.03Western Delta 5.97 0.08 0.00

Delta Exports and Juvenile Chinook Salmon Rearing and Migration. Although the survival of Merced River hatchery smolts from 1996 to 2002 was not correlated with Delta export rates between 1,529 cfs and 3,163 cfs (SJRGA 2003), mortality occurs as a result of entrainment at the pumping facilities and predation losses at Clifton Court Forebay (Brandes and McLain 2001). Many of the marked fish were observed at the pumping facilities when they were released into

87


the upper Old River (average 19%) compared to those released at Dos Reis (average 3%; Brandes and McLain 2001). In addition, early smolt survival studies with Feather River Hatchery Fish indicate that smolt survival was low when Delta exports were high, but water temperatures should have been suitable. In mid April 1991, the estimated absolute survival of smolts from the Feather River Hatchery was only 9.4%, when total Delta exports were 7,880 cfs, Vernalis flows were 809 cfs, and the mean water temperature near Stockton was 61.2 oF for a 10-day period following the fishes’ release.

Reducing Delta export rates to between 10% and 100% of San Joaquin River flows at Vernalis between mid-April and mid-May appears to have resulted in a limited increase in adult recruitment to the Stanislaus River in five of seven years studied (Appendix 1). Although it is possible that the CWT smolt survival studies do not represent the true survival rates of naturally produced fish and the 30-day reductions in exports actually provide little benefit, it is also possible that increased export rates between January and mid-April have offset the benefits.

Head of the Old River Barrier and Juvenile Chinook Salmon Rearing and Migration. DWR is proposing to install a permanent operable concrete and steel barrier at the head of the Old River as part of the South Delta Improvements Program and will release a combined draft environmental impact report/environmental impact statement for this project in 2003 (http://sdelta.water.ca.gov/). The HORB may improve survival up 400 % by increasing San Joaquin River flows downstream of the Old River, reducing water temperatures in the Stockton deep-water ship channel, and reducing entrainment. In May 1996, the HORB was not installed and only about 39% of Vernalis flows (2,475 cfs) remained in the mainstem near Stockton. At the same time, water temperature in the mainstem near Stockton increased by about 3°F which indicates that the diversion of flow into the Old River may increase temperatures downstream in the San Joaquin River; the mean afternoon water temperature upstream of the Old River at Mossdale was 64.2°F, while downstream of the Old River near Stockton at Burns Cutoff DWR monitoring station was 67.3°F. Under these conditions in 1996 without the barrier, the survival of Merced River hatchery smolts was only 15%, whereas, higher flow and lower temperature conditions attributed to installation of the barrier in 1997 resulted in a smolt survival rate of 46% based on ocean recoveries (SJRGA 2002). In contrast, during the 2000 and 2001 studies when the barrier was installed and Stockton flows ranged between 4,000 cfs and 6,100 cfs, water temperatures were only slightly higher (<1°F) at the DWR monitoring station near Stockton than at Mossdale (SJRGA 2001, 2002); temperature near Stockton was 64.2°F.

However, in spring 1994, 1997, and 2000 the HORB was installed with up to six open culverts and had no obvious effect on the number of recruits-per-spawner compared to 1995, 1996, 1998, and 1999, when the HORB was not installed (Figures 28 and 29). Although it is possible that the CWT smolt survival studies do not represent the true survival rates of naturally produced fish and the barrier actually provides little or no benefit, it is also possible that the barrier needs to be installed for a longer period than from just mid-April to mid-May. Several additional recruit-per-spawner estimates and VAMP survival estimates are needed to determine whether installing the HORB between April 15 and May 15 increases juvenile survival.

Although the HORB may create better survival conditions, other environmental conditions may influence the ability, and/or the magnitude, that the HORB may increase survival. For example, the HORB would probably not improve smolt survival if air temperatures were either: (1) low enough to maintain suitable water temperatures near Stockton at low flows, or (2) so high that

88

http://sdelta.water.ca.gov/


water temperatures near Stockton would be lethal even at high flows.

3.3 OCEAN SURVIVAL

3.3.1. Ocean Climate

In spring 1997, when extensive flooding occurred and presumably juvenile salmonid survival was high, studies by MacFarlane and Norton (2002) indicated that juvenile fall-run Chinook salmon spent about 40 days feeding and migrating through the San Francisco Estuary. During their migration through the estuary, they stored lipids for energy reserves, but exhibited relatively slow growth in length and a substantial decline in condition factor compared to juvenile Chinook in estuaries in the Northwest. Although the process of smoltification can result in declines in condition factor, gill Na+, K+-ATPase activity in a 1999 study indicated that smoltification was largely completed by the time the juveniles entered the San Francisco Estuary (MacFarlane and Norton 2002). MacFarland and Norton (2002) speculated that the loss of extensive estuary embayments reduced the availability of important food resources, particularly plankton, that are abundant in the northern estuaries. After the juvenile Chinook salmon entered the Gulf of the Farallones between May and June in 1997, they intensified their feeding and rapidly utilized their lipid reserves (triacylglycerols) while they grew rapidly in length and weight (MacFarlane and Norton 2002). This behavior suggests that food availability, primarily fish larvae, in the Gulf of the Farallones could be another critical factor for survival of juvenile Central Valley Chinook salmon.

Changes in ocean climate appear to affect salmon early in their marine life history and long-term records indicate that there are 15- to 25-year cycles of warm and cool periods in the northeastern Pacific Ocean that are strongly correlated with marine ecosystem productivity (Hare and Francis 1995). Cool cycles prevailed from 1947-1976 while warm cycles dominated from 1977 through at least the mid-1990s (Mantua and others 1997). During the mid 1970s, a major shift occurred from a colder to warmer-than average regime in the California current (MacCall and others 1992; Francis and others 1998). This shift was accompanied by a drop in coastal zooplankton abundance by as much as 70%, vigorous recovery of the depleted sardine population off Southern California (Hayward and others 1992; Francis and others 1998), and decreases in the harvest of spring-run Chinook and coho salmon off the coast of Washington, Oregon, and California (Mantua and others 1997). Salmon landings off the California coast, which includes mostly Chinook salmon and relatively few coho, followed a similar pattern to the one reported by Mantua and others (1997) for West Coast coho and spring-run salmon: California salmon landings were high during the cool cycles from 1916 to 1925 (mean 5,062 tons) and from 1944 to 1982 (mean 4,100 tons) and low during the warm cycles from 1926 to 1943 (mean 2,632 tons) and from 1983 to 1997 (mean 2,865 tons). The coastal warming that occurred in the mid 1970s is believed to have caused increased stratification in the California Current, a sharper thermocline with less vertical displacement of nutrient rich water due to coastal upwelling, a reduction in the duration of upwelling conditions, and a reduction in nutrients and/or zooplankton abundance off the California coast (Francis and others 1998).

However, ocean climate does not appear to have a strong influence on adult recruitment to the

89


salmon population in the Stanislaus River. Mean recruitment to the Stanislaus River only declined from 13,768 fish for the productive 1946 to 1976 period to 10,791 fish for the non-productive 1977 to 1997 period. The correlation analysis by Mesick (Appendix 1) suggests that the effect of flow (and presumably water temperature and dissolved oxygen) in the San Joaquin Delta overrides the effect of ocean climate on smolt survival.

3.3.2 Ocean Harvest

Chinook salmon from the Stanislaus River are primarily harvested in the ocean. The commercial ocean troll fishery off the California coast grew rapidly in the mid 1940s with an increase in the number and size of boats and use of power puller mechanisms for the lines, called gurdies (California Bureau of Marine Fisheries 1949). The commercial salmon landings off the California coast increased from a mean of 2,556 tons from 1932 to 1943 to 5,254 tons from 1944 to 1949 probably in response to the increased fishing pressure and an increase in salmon production in the Sacramento River basin (California Bureau of Marine Fisheries 1949, Fry 1961). From 1950 to 1995, harvest averaged about 3,500 tons of salmon, which is about two-thirds of the total salmon production of all the Central Valley rivers (Boydstun 2001).

There was a commercial drift gill net fishery in the Pittsburg-Martinez area that increased from about 150 boats in the mid-1930s to 240 boats in 1947 (California Bureau of Marine Fisheries 1949). The season was legally closed from June 16th to August 9th and again from September 27th

to November 14th (California Bureau of Marine Fisheries 1949). The annual Chinook salmon catch of the gill-net fishery averaged 1,141 tons from 1946 to 1952. The gill net fishery was completely closed in 1958.

The mean catch of the ocean sport fishery is about 20% of the total number of Chinook salmon produced in the Central Valley from 1947 to 2002 (Appendix 1). Catch data are not available for the sport fishery prior to 1947.

High rates of ocean harvest reduce the abundance of four-year-old and five-year-old Central Valley Chinook salmon that return to spawn. A substantial reduction in the number of these large spawners has several implications (Vogel, personal communication, X). First, the loss of multiple-age populations causes the salmon runs to be particularly vulnerable to natural disasters (e.g., floods and droughts) that devastate single-age spawning stocks. Second, the large four-year-old females tend to dig deeper redds which helps improve the permeability of the spawning beds. Finally, four-year-old females produce more eggs than do three-year-olds and the reduction in their numbers has reduced the fecundity to the overall populations. Reduced fecundity was a particular problem whenever environmental conditions reduced recruitment to very low levels and consequently stock was reduced two and possibly three years later. Stock was less than 1,500 spawners, which probably limited recruitment, during 46% of the years in the Stanislaus River from 1958 to 2002 (Appendix 1).

The California ocean salmon fisheries are managed by the Pacific Fishery Management Council (Council) under the federal Magnuson-Stevens Fishery Conservation and Management Act. Although the original plan developed by the Council in 1977 had an escapement goal for San Joaquin Basin salmon, the goal was removed in 1984 because Delta exports were affecting the run (Boydstun 2001). Nevertheless, harvest, as estimated by the Central Valley Index (CVI), has

90


When?


been reduced from an average of 0.74 from 1990 to 1995 to an average of 0.47 from 1998 to 2001 to meet escapement goals for the Sacramento River Basin.

91


4. LITERATURE CITED

Adams, B.L., W.S. Zaugg and L.R. McLain. 1975. Inhibition of salt water survival and Na-K-ATPase elevation in steelhead trout (Salmo gairdnerii) by moderate water temperatures. Trans. Am. Fish. Soc. 104:766-769.

Aceituno, M.E. 1993. The relationship between instream flow and physical habitat availability for Chinook salmon in the Stanislaus River. U.S. Fish and Wildlife Service, Sacramento, California.

Allan, J.D. 1995. Stream ecology: structure and function of running waters. Chapman & Hall, London. 388 pp.

Arkoosh, M.R., E. Casillas, P. Huffman, E. Clemons, J. Evered, J.E. Stein, and U. Varanasi. 1998. Increased susceptibility of juvenile Chinook salmon from a contaminated estuary to Vibrio anguillarum. Trans. Am. Fish. Soc. 127:360–374.

Bailey, E.D. 1954. Time pattern of 1953-54: Migration of salmon and steelhead into the upper Sacramento River. Calif. Dept. Fish and Game, Region 1, Redding, CA.

Baker, P.F., T.P. Speed, and F.K. Ligon. 1995. Estimating the influence of temperature on the survival of Chinook salmon smolts (Oncorhynchus tshawytscha) migrating through the Sacramento/San Joaquin River Delta of California. Can. J. Fish. Aquat. Sci. 52: 855-863.

Barnhart, R.A. 1986. Species profiles: Life histories and environmental requirements of coastal fishes and invertebrates (Pacific Southwest)—steelhead. USFWS Bio. Rep. 82(11.60). 21 pp.

Barnhart, R.A. 1991. Steelhead (Oncorhynchus mykiss). In: J. Stolz and J. Schnell (eds.), Trout: The Wildlife Series. Stackpole Books, Harrisburg, PA. 370 pp.

Bell, M.C. 1986. Fisheries Handbook of Engineering Requirements and Biological Criteria. Fish Passage Development and Evaluation Program. U.S. Army Corps of Engineers, North Pacific Division, Portland, OR. 290 pp.

Bell, M.C. 1991 (revised). Fisheries Handbook of Engineering Requirements and Biological Criteria. Fish Passage Development and Evaluation Program. U.S. Army Corps of Engineers, North Pacific Division, Portland, OR.

Bjornn, T.C. 1968. Survival and emergence of trout and salmon in various gravel-sand mixtures. In: Proceedings of a Forum on the Relation Between Logging and Salmon, pp. 80-88. Amer. Inst. Fisheries Research Biologists and Alaska Dept. Fish and Game, Juneau, AK.

Bjornn, T.C., and D.W. Reiser. 1991. Habitat requirements of salmonids in streams. Am. Fish. Soc. Pub. 19:83-138.

92


Boles, G.L., S.M. Turek, C.C. Maxwell, and D.M. McGill. 1988. Temperature effects on Chinook salmon (Oncorhynchus tshawytscha) with emphasis on the Sacramento River: A literature review. Calif. Dept. Water Resources, Northern District, Red Bluff, CA. 43 pp.

Bovee, K.D. 1978. Probability-of-use criteria for the family Salmonidae. Instream Flow Information Paper No.4, U.S. Fish and Wildlife Service. FWS/OBS-78/07. 80 pp.

Boydstun, L.B. 2001. Ocean salmon fishery management. In: R.L. Brown (ed.), Contributions to the Biology of Central Valley Salmonids. Calif. Dept. Fish and Game, Fish Bulletin 179(2): 183-195.

Brandes, P.L. and J.S. McLain. 2001. Juvenile Chinook salmon abundance, distribution, and survival in the Sacramento-San Joaquin Estuary. In: R.L. Brown (ed.), Contributions to the Biology of Central Valley Salmonids. Calif. Dept. Fish and Game, Fish Bulletin 179(2):39-138.

Brett, J.R. 1952. Temperature tolerance in young Pacific salmon, genus Oncorhynchus. J. Fish. Res. Board of Canada 9:265-323.

Brett, J.R., W.C. Clarke, and J.E. Shelbourn. 1982. Experiments on thermal requirements for growth and food conversion efficiency of juvenile Chinook salmon, Oncorhynchus tshawytscha. Can. Tech. Rep. Fish. Aquat. Sci. 1127. 29 pp.

Brown L. 1996. Aquatic biology of the San Joaquin-Tulare basins, California: Analysis of available data through 1992. Report prepared in cooperation with the National Water-Quality Assessment Program by the U.S. Geological Survey. Water Supply Paper 2471.

Brown, L.R., and P.B. Moyle. 1981. The impact of squawfish on salmonid populations: A review. N. American J. Fish. Manage. 1:104-111.

Bumgarner, J., G. Mendel, D. Milks, L. Ross, M. Varney, and J. Dedloff. 1997. Tucannon River Spring Chinook Salmon Hatchery Evaluation Program: 1996 Annual report. Washington Department of Fish and Wildlife Hatcheries Program Assessment and Development Division. Report #H97-07. Produced for US Fish and Wildlife Service, Cooperative Agreement 14-48-0001-96539.

Busby, P.J., T.C. Wainwright, G.J. Bryant, L.J. Lierheimer, R.S. Waples, F.W. Waknitz, and I.V. Lagomarsino. 1996. Status Review of West Coast Steelhead from Washington, Idaho, Oregon, and California. NOAA Tech. Memo 27, National Marine Fisheries Service, Seattle, WA. 261 pp.

CALFED. 1999. CALFED’s Comprehensive Monitoring, Assessment, and Research Program for Chinook Salmon and Steelhead in the Central Valley Rivers. CALFED-Bay Delta Program, Sacramento, CA.

California Bureau of Marine Fisheries. 1949. The commercial fish catch of California for the year 1947 with an historical review 1916-47. Calif. Division of Fish and Game, Fish Bulletin 74: 1-223.

93


[CDFG] California Department of Fish and Game. 1965. California Fish and Wildlife Plan. Three volumes. Calif. Dept. Fish and Game, Sacramento, CA.

CDFG. 1991 to 1998. Annual Performance Reports, Fiscal Years 1987–1997, San Joaquin River Chinook Salmon Enhancement Project. Sport Fish Restoration Act, Project F–51–R–4, Sub Project Number IX, Study Number 5, Jobs 1 through 7. Calif. Dept. Fish and Game, Region 4, Fresno, CA.

CDFG. 1992. Interim actions to reasonably protect San Joaquin fall-run Chinook salmon. (WRINT-DFG Exhibit 25). Prepared for the Water Rights Phase of the State Water Resources Control Board Bay-Delta Hearing Proceedings, June 22, 1992 in Sacramento, CA.

CDFG. 1993. Restoring Central Valley streams: A plan for action. Calif. Dept. Fish and Game, Inland Fisheries Division, Sacramento, CA

CDFG. 1998a. Annual Performance Report, Fiscal Year 1996–1997, San Joaquin River Chinook Salmon Enhancement Project. Sport Fish Restoration Act, Project F–51–R–6, Sub Project Number IX, Study Number 5, Jobs 1 through 7. Calif. Dept. Fish and Game, Region 4, Fresno.

CDFG. 1998b. California Salmonid Stream Habitat Restoration Manual, Third Edition. Calif. Dept. Fish and Game, Inland Fisheries Division, Sacramento, CA. 495 pp.

CDFG. 1998c. Report to the Fish and Game Commission: a status review of the spring-run

Chinook salmon (Oncorhynchus tshawytscha) in the Sacramento River Drainage. Candidate Species Status Report 98-01. June 1998.

CDFG. 2002a. Annual report 2001/2002: San Joaquin River salmon enhancement. Calif. Dept. Fish and Game, Region 4, Fresno, CA.

CDFG. 2002b. Review Draft Russian River Basin Fisheries Restoration Plan, July 2002. Calif. Dept. Fish and Game. Available from Internet at http//:hopland.uchrec.org/ihrmp/publications/draftbp/BASINP.0702.00.pdf

[CMC and others] Carl Mesick Consultants, Aquatic Systems Research, and Thomas R. Payne & Associates. 1996. Spawning habitat limitations for fall-run Chinook salmon in the Stanislaus River between Goodwin Dam and Riverbank. Review draft report prepared for Neumiller & Beardslee and the Stockton East Water District. 1 July 1996.

CMC. 1997. A fall 1996 study of spawning habitat limitations for fall-run Chinook salmon in the Stanislaus River between Goodwin Dam and Riverbank. Review draft report prepared for Neumiller & Beardslee and the Stockton East Water District. Carl Mesick Consultants, El Dorado, California. 3 June 1997.

94


CMC. 2001. Task 3 pre-project evaluation report, Knights Ferry Gravel Replenishment Project. Final report produced for the CALFED Bay Delta Program and the Stockton East Water District. Carl Mesick Consultants, El Dorado, California. Revised 20 July 2001.

CMC. 2002a. Task 5 initial post-project evaluation report, fall 2000, Knights Ferry Gravel Replenishment Project. Final report produced for the CALFED Bay Delta Program and the Stockton East Water District. Carl Mesick Consultants, El Dorado, California. 14 January 2002.

CMC. 2002b. Task 6 second year post-project evaluation report, fall 2000, Knights Ferry Gravel Replenishment Project. Final report produced for the CALFED Bay Delta Program and the Stockton East Water District. Carl Mesick Consultants, El Dorado, California. 20 February 2002.

Castro-Santos, T. and A. Haro. 2000. Sprinting performance of upstream migratory fishes.

Chadwick, H.K. 1982. Biological effects of water projects on the Sacramento-San Joaquin estuary. In: W. Kockelman, T. Conomos, and A. Leviton (eds.), San Francisco Bay: Use and protection, pp. 215-219. Amer. Assoc. for the Advancement of Science, Pac. Div.

Chambers, J. 1956. Fish passage development and evaluation program. Progress Report No. 5. U.S. Army Corps of Engineers, North Pacific Division, Portland, OR.

Clark, G.H. 1929. Sacramento-San Joaquin salmon (Oncorhynchus tschawytscha) fishery of California. Calif. Division of Fish and Game, Fish Bulletin No. 17:1-73.

Clarke, W.C. and J.E. Shelbourn. 1985. Growth and development of seawater adaptability by juvenile fall Chinook salmon (Oncorhynchus tshawytscha) in relation to temperature. Aquaculture 45:21-31.

Coble, D.W. 1961. Influence of water exchange and Dissolved oxygen in redds on the survival of steelhead trout embryos. Trans. Amer. Fish. Soc. 90:469-474.

Coutant, C.C. 1970. Thermal resistance of adult coho (Oncorhynchus kisutch) and jack Chinook (O. tshawytscha) salmon, and adult steelhead trout (Salmo gairdneri) from the Columbia River. Battelle Memorial Inst., Pac. Northwest Lab., Richland, WA. Rep. No. BNWL-1508, UC-48. 24 p.

Cramer, F.K. and D.F. Hammack. 1952. Salmon research at Deer Creek, California. U.S. Fish and Wildlife Service Special Scientific Reports, Fisheries No. 67. 16 pp.

Cramer, S.P. 1990. Contribution of Sacramento Basin hatcheries to ocean catch and river escapement of fall Chinook salmon. Prepared for the Calif. Dept. of Water Resources by S.P. Cramer & Associates, Gresham, OR.

Cramer, S.P. and D.B. Demko. 1993. Evaluation of juvenile Chinook entrainment at six unscreened water diversions along the Sacramento River by Reclamation District 108. S.P. Cramer & Associates, Gresham, CA.

95


Demko D.B. and S.P. Cramer. 1997. Outmigrant trapping of juvenile salmonids in the lower Stanislaus River Caswell State Park site, 1996. Report prepared for the U.S. Fish and Wildlife Service’s Anadromous Fish Restoration Program by S.P. Cramer & Associates under contract with CH2M Hill, Sacramento, CA.

Demko D.B., C. Gemperle, S.P. Cramer, and A. Phillips. 1998. Evaluation of juvenile Chinook behavior, migration rate, and location of mortality in the Stanislaus River through the use of radio tracking. Report prepared for Tri-dam Project by S.P. Cramer & Associates, Gresham, OR.

Demko D.B., C. Gemperle, S.P. Cramer, and A. Phillips. 1999. Outmigrant trapping of juvenile salmonids in the lower Stanislaus River Caswell State Park site, 1998. Report prepared for the U.S. Fish and Wildlife Service’s Anadromous Fish Restoration Program by S.P. Cramer & Associates under contract with CH2M Hill, Sacramento, California.

Demko, D.B., C. Gemperle, A. Phillips, and S.P. Cramer. 2000. Outmigrant trapping of juvenile salmonids in the lower Stanislaus River Caswell State Park Site, 1999. Report prepared for the U.S. Fish and Wildlife Service’s Anadromous Fish Restoration Program by S.P. Cramer & Associates under contract with CH2M Hill, Sacramento, California.

[DWR] California Department of Water Resources. 1994. San Joaquin River tributaries spawning gravel assessment: Stanislaus, Tuolumne, Merced rivers. Draft memorandum prepared for the Calif. Dept. Fish and Game by the Calif. Dept. Water Resources, Northern District, Red Bluff, CA. Contract number DWR 165037.

DWR. 1999. Suisun Marsh salinity control gates annual fisheries monitoring report for 1997. Memorandum report. Calif. Dept. Water Resources, Sacramento, CA.

Dettman, D.H. and D.W. Kelley. 1987. The roles of Feather and Nimbus salmon and steelhead hatcheries and natural reproduction in supporting fall run Chinook salmon populations in the Sacramento River basin. Prepared for Calif. Dept. Water Resources by D.W. Kelley and Associates, Newcastle, CA.

[EA] EA Engineering, Science, and Technology. 1992. Lower Tuolumne River predation study report in Appendix 22, Report of Turlock Irrigation District and Modesto Irrigation District Pursuant to Article 39 of the License for the Don Pedro Project. Report prepared for the Turlock Irrigation District and the Modesto Irrigation District by EA Engineering, Science, and Technology.

Ekman, E. 1987. Report on adult spring-run salmon surveys, 1986 and 1987. Prepared for Lassen National Forest.

Erkkila, L.F., J.W. Moffett, O.B. Cope, B.R. Smith, and R.S. Nielson. 1950. Sacramento-San Joaquin Delta fishery resources: effects of Tracy pumping plant and Delta Cross Channel. U.S. Fish and Wildlife Service Special Scientific Report, Fisheries No. 56.

Everest, F.H. 1973. Ecology and management of summer steelhead in the Rogue River. Oregon State Game Comm., Fishery Research Report 7, Corvallis, OR. 48 pp.

96


Fisher, F.W. 1994. Past and present status of Central Valley Chinook salmon. Consv. Biol. 8:870-873.

Fisheries Foundation. 2002. Stanislaus River anadromous fish surveys 2000-2001. Draft report produced for the U.S. Fish and Wildlife Service, Sacramento, CA. April 2002.

Folmar, C.F. and W.W. Dickhoff. 1980. The parr-smolt transformation (smoltification) and seawater adaptation in salmonids. Aquaculture 21:1-37.

Francis, R.C., S.R. Hare, A.B. Hollowed, and W.S. Wooster. 1998. Effects of interdecadal climate variability on the oceanic ecosystems of the NE Pacific. Fish Oceanogr. 7:1-21.

Fry, D.H., Jr. 1961. King salmon spawning stocks of the California Central Valley, 1940-1959. Calif. Fish and Game 47(1):55-71.

Goodbred S.L., R.J. Gilliom, T.S. Gross, N.P. Denslow, W.L. Bryant, and T.R. Schoeb. 1997. Reconnaissance of 17B–estradiol, 11–ketotestosterone, vitellogenin, and gonad histopathology in common carp of United States streams: Potential for contaminant-induced endocrine disruption. U.S. Geological Survey Open–File Report 96–627. Sacramento, CA.

Gregory, R.S. and C.D. Levings. 1998. Turbidity reduces predation on migrating juvenile Pacific salmon. Trans. Am. Fish. Soc. 127: 275-285.

Guignard, J. 2003. 2000 Stanislaus River Summer Gill Netting. Draft summary. Calif. Dept. Fish and Game, Fresno, CA.

Guo, L., C. Nordmark, F. Spurlock, B. Johnson, L. Li, M. Lee, and K. Goh. 2003. Semi-Empirical prediction of pesticide loading in the Sacramento and San Joaquin Rivers during winter storm seasons. State of California, California Environmental Protection Agency, Department of Pesticide Regulation, Environmental Monitoring Branch.

Hallock, R.J., W.F. Van Woert, and L. Shapovalov. 1961. An evaluation of stocking hatchery-reared steelhead rainbow trout (Salmo gairdnerii gairdnerii), in the Sacramento River system. Calif. Dept. Fish and Game, Fish Bulletin 114, 73 pp.

Hallock R.J., R.F. Elwell, and D.H. Fry, Jr. 1970. Migrations of adult king salmon Oncorhynchus tshawytscha in the San Joaquin Delta; as demonstrated by the use of sonic tags. Calif. Dept. Fish and Game, Fish Bulletin 151.

Hallock, R.J. and R.R. Reisenbichler. 1979. Evaluation of returns from Chinook salmon, Oncorhynchus tshawytscha, released as fingerlings from Coleman and Nimbus hatcheries and in the Sacramento River estuary. Unpublished office report available from Dept. of Fish and Game, Inland Fisheries Div., 1416 Ninth St., Sacramento, CA 95814.

Hallock, R.J. 1989. Upper Sacramento River steelhead, Oncorhynchus mykiss, 1952-1988. Report prepared for U.S. Fish and Wildlife Service, Red Bluff, CA. 86 pp.

97


Hanson, C.R. 1991. Acute temperature tolerance of juvenile Chinook salmon from the Mokelumne River. Hanson Environmental, Inc., Walnut Creek, CA.

Hare S.R. and R.C. Francis. 1995. Climate change and salmon production in the northeast Pacific Ocean. In: R.J. Beamish (ed.), Climate Change and Northern Fish Populations. Can. Spec. Publ. Fish. Aquat. Sci. 121:357–372.

Hayward, T.R. Smith, D. Ainley, P. Bernal, M. Eakin, R. Haney, A. Hollowed, P. Hsueh, W. Pearcy, I. Perry, L. Sautter, F. Schwing, and T. Strub. 1992. El Nino/southern oscillation (ENSO) effects within the California current system. Working Group Report in Global Ocean Ecosystems Dynamics and Climate Change (GLOBEC). Eastern Boundary Current Program Report on Climate Change and the California Current Ecosystem. Report Number 7. Workshop held 17-20 September 1992 at Bodega Marine Laboratory of the University of California.

Hinze, J.A. 1959. Annual Report: Nimbus salmon and steelhead hatchery, fiscal year 1957-1958. Calif. Dept. Fish and Game, Inland Fish Division, Admin. Rept. 59-4.

Healey, M.C. 1986. Optimum size and age at maturity in Pacific salmon and effects of size-selective fisheries. In: D.J. Meerburg (ed.), Salmonid Age at Maturity. Can. Spec. Pub. Fish. Aquat. Sci. 89:39-52.

Healey, M.C. 1991. Life history of Chinook salmon. In: C. Groot and L. Margolis (eds.), Pacific Salmon Life Histories, pp 311-394. University British Columbia Press, Vancouver.

Herren, J.R. and S.S. Kawasaki. 2001. Inventory of water diversions in four geographic areas in California’s Central Valley. In: R.L. Brown (ed.), Contributions to the Biology of Central Valley Salmonids. Calif. Dept. Fish and Game, Fish Bulletin 179(2):343-355.

Hoar, W.S. 1976. Smolt transformation: evolution, behavior, and physiology. J. Fish. Res. Board Can. 33:1234-1252.

Houston, A.H. 1982. Thermal effects upon fishes. National Research Council of Canada. Committee on Scientific Criteria for Environmental Quality. Report NRCC No. 18566.

[IEP] Interagency Ecological Program. 1999. Monitoring, assessment, and research on Central Valley steelhead: status of knowledge, review, of existing programs, and assessment of needs. Interagency Ecological Program Steelhead Project Workteam, Sacramento, CA.

Kjelson, M.A., P.F. Raquel, F.W. Fisher. 1982. Life history of fall Chinook salmon, Oncorhynchus tshawytscha in the Sacramento-San Joaquin estuary, California. In: V.S. Kennedy (ed.), Estuarine Comparisons, pp. 393-411. Academic Press, New York, NY.

Kondolf, G.M. 2000. Assessing Salmonid Spawning Gravel Quality. Trans. Am. Fish. Soc. 129:262-281.

98


Kondolf, G.M., A. Falzone, and K.S. Schneider. 2001. Reconnaissance-level assessment of channel change and spawning habitat on the Stanislaus River below Goodwin Dam. Report to the U.S. Fish and Wildlife Service, Sacramento, CA. 22 March 2001.. Bull. 87:239-264.

Large, A.R.G. and G. Petts. 1996. Rehabilitation of River Margins. In: G. Petts and P. Calow (eds.), River Restoration: Selected Extracts from the Rivers Handbook, pp. 106-123. Blackwell Science Ltd., Oxford.

Lee, D. 2000. The Sacramento-San Joaquin Delta largemouth bass fishery. Interagency Ecological Program Newsletter 13(3):37-40.

Leidy and Li. 1987. Analysis of river flows necessary to provide water temperature requirements of anadromous fishery resources of the lower American River.

Levy, D.A., and T.G. Northcote. 1982. Juvenile salmon residency in a marsh area of the Fraser River estuary. Can. J. Fish. Aquat. Sci. 39:270-276.

MacCall A, Kremer P, Graham W, Haney R, Hollowed A, Mackas D, Ohman M, Powell T, Rau G, Rice J, Schumacher J, Shapiro L, Smith P, Welling L, and Woehler E. 1992. Major shifts in species composition and ecosystem structure. Working Group Report in Global Ocean Ecosystems Dynamics and Climate Change (GLOBEC). Eastern Boundary Current Program Report on Climate Change and the California Current Ecosystem. Report Number 7. Workshop held 17-20 September 1992 at Bodega Marine Laboratory of the University of California.

MacFarlane, B. 1999. Physiological ecology of juvenile Chinook salmon in the San Francisco Estuary and Gulf of the Farallones. Presentation at the Interagency Ecological Program Annual Workshop, 26 February 1999, Asilomar Conference Center, Pacific Grove, California.

MacFarlane, R.B. and E.C. Norton. 2002. Physiological ecology of juvenile Chinook salmon (Oncorhynchus tshawytscha) at the southern end of their distribution, the San Francisco Estuary and Gulf of the Farallones. Calif. Dept. Fish and Game, Fish. Bulletin 100:244-257.

Mantua N.J., S.R. Hare, Y. Zhang, J.M. Wallace, and R.C. Francis. 1997. A Pacific interdecadal climate oscillation with impacts on salmon production. Bulletin of the American Meteorological Society 78:1069-1079.

Marcotte, B.D. 1984. Life history, status, and habitat requirements of spring-run Chinook salmon in California. Lassen National Forest, Chester Ranger District, Chester, CA. 34 pp.

Marine, K.R. and J.J. Cech, Jr. 1992. An investigation of the effects of elevated water temperature on some aspects of the physiological and ecological performance of juvenile chinook salmon: Implications for management of California Central Valley salmon stocks. A final report to the Interagency Ecological Studies Program for San Francisco

99


Bay/Delta and the California Dept. of Water Resources. Prepared by Dept. Wildlife and Fisheries Biology, U.C. Davis, CA.

Marine, K.M. 1997. Effects of elevated water temperature on some aspects of the physiological and ecological performance of juvenile Chinook salmon (Oncorhynchus tshawytscha): implication for management of California’s Central Valley salmon stocks. Masters Thesis, University of California, Davis.

McBain and Trush. 2003. Coarse sediment management plan for the lower Tuolumne River. Draft report prepared for the Tuolumne River Technical Advisory Committee, Turlock and Modesto Irrigation Districts, USFWS Anadromous Fish Restoration Program, and the CALFED Bay-Delta Authority. 5 May 2003.

McEwan, D., and T.A. Jackson. 1996. Steelhead restoration and management plan for California. Calif. Dept. Fish and Game Management Report. Avaiallbe from the Internet at http//:www.dfg.ca.gov/nafwb/pubs/swshplan.pdf

McEwan, D.R. 2001. Central Valley steelhead. In: R.L. Brown (ed.), Contributions to the Biology of Central Valley Salmonids. Calif. Dept. Fish and Game, Sacramento, CA. Fish Bulletin 179(1):1-44.

Merz, J.E. and C.D. Vanicek. 1996. Comparative feeding habits of juvenile Chinook salmon, steelhead, and Sacramento squawfish in the lower American River, California. Calif. Fish Game 82: 149-159.

Mesick, C.F. 2001a. Studies of spawning habitat for fall-run Chinook salmon in the Stanislaus River between Goodwin Dam and Riverbank from 1994 to 1997. In: R.L. Brown (ed.), Contributions to the Biology of Central Valley Salmonids. Calif. Dept. Fish and Game, Fish Bulletin 179(2):217-252.

Mesick, C.F. 2001b. The effects of San Joaquin River flows and Delta export rates during October on the number of adult San Joaquin Chinook salmon that stray. In: R.L. Brown (ed.), Contributions to the Biology of Central Valley Salmonids. Calif. Dept. Fish and Game, Fish Bulletin 179(2):139-161.

Milner, A.M. and R.G. Bailey. 1989. Salmonid colonization of new streams in Glacier Bay National Park, Alaska. Aquaculture and Fisheries Management 20: 179-192.

Moore, T.L. 1997. Condition and feeding of juvenile Chinook salmon in selected intermittent tributaries of the upper Sacramento River. Master’s Thesis, Calif. State Univ., Chico.

Moyle, P.B., J.E. Williams, and E.D. Wikramanayake. 1989. Fish species of special concern of California. Submitted to Calif. Dept. Fish and Game, Sacramento, CA. Contract No. 2128IF. 272 pp.

Moyle, P.B. 2002. Inland Fishes of California. University of California Press, Berkeley, CA. 502 pp.

100


Murphy, B.R., D.W. Willis and T.A. Springer. 1991. The relative weight index in fisheries management: status and needs. Fisheries 16(2).

Myers, J.M., R.G. Kope, G.J. Bryant, D. Teel, L.J. Lierheimer, T.C. Wainright, W.S. Grant, F.W. Waknitz, K. Neely, S.T. Lindley, and R.S. Waples. 1998. Status review of Chinook salmon from Washington, Idaho, Oregon, and California. NOAA Tech. Memo NMFS-NWFSC-35, National Marine Fisheries Service, Seattle, WA. 443 pp.

Myrick, C.A. and J.J. Cech, Jr. 2001. Temperature effects on Chinook salmon and steelhead: a review focusing on California's Central Valley populations. Bay-Delta Modeling Forum Technical Publication 01-1 available from the Internet at http://www.sfei.org/modelingforum/..

Nichols, K. and J.S. Foott. 2002. Health monitoring of hatchery and natural fall-run Chinook salmon juveniles in the San Joaquin River and tributaries, April–June 2001. FY 2001 Investigation Report by the U.S. Fish and Wildlife Service, California-Nevada Fish Health Center, Anderson, CA.

Nichols, K. 2002. Merced River PKD Survey – Spring 2002. Memorandum to the San Joaquin Basin Fish Health Information Distribution List dated December 6, 2002. U.S. Fish and Wildlife Service, California-Nevada Fish Health Center, Anderson, CA.

[NOAA Fisheries] National Marine Fisheries Service. 2000. Biological opinion for Banta Carbona Irrigation District fish screen project. Prepared for U.S. Bureau of Reclamation, Mid-Pacific Region by NOAA Fisheries, Southwest Region, Long Beach, CA.

NOAA Fisheries. 2002. Biological opinion for the Central Valley Project (CVP) and State Water Project (SWP) operations, April 1, 2002 through March 31, 2004. Prepared for U.S. Bureau of Reclamation, Mid-Pacific Region by NOAA Fisheries, Southwest Region, Long Beach, CA.

Nobriga, M. M. Chotkowski, and R. Baxter. 2003. Baby steps toward a conceptual model of predation in the Delta: preliminary results from the shallow water habitat predator-prey dynamics study. Interagency Ecological Program Newsletter 16(1): 19-27.

Patten, B.G. 1971. Predation by sculpins on fall Chinook salmon, Oncorhynchus tshawytscha, fry of hatchery origin. U.S. Nat. Mar. Fish. Serv. Spec. Sci. Rep. Fish. 621:14 p.

Peake, S. and R.S. McKinley. 1998. A re-evaluation of swimming performance in juvenile salmonids relative to downstream migration. Can. J. Fish. Aquat. Sci./J. Can. Sci. Halieut. Aquat. 55(3): 682-687.

Phillips, R.W. and H.J. Campbell. 1961. The embryonic survival of coho salmon and steelhead trout as influenced by some environmental conditions in gravel beds. Annual Rep. Pac. Mar. Fish. Comm. 14: 60-73.

101

http://www.sfei.org/modelingforum/


Phillips, R.W., R.L. Lantz, E.W. Claire, and J.P. Moring. 1975. Some effects of gravel mixtures on emergence of coho salmon and steelhead trout fry. Trans. Amer. Fish. Soc. 140: 461-466.

Pickard, A., A. Grover, and F.A. Hall, Jr. 1982. An evaluation of predator composition at three locations on the Sacramento River. Interagency Ecological Study Program for the Sacramento-San Joaquin Estuary. Technical Report 2.

Platts, W.S., W.F. Megahan, and G.W. Minshall. 1979. Methods for evaluating stream, riparian, and biotic conditions. U.S. Dept. Agriculture General Technical Report INT-138. Ogden, UT. 78 pp.

Puckett, L.K. and R.N. Hinton. 1974. Some measurements of the relationship between streamflow and king salmon spawning gravel in the main Eel and South Fork Eel rivers. Calif. Dept. Fish and Game, Env. Serv. Br., Admin. Rept. 74-1.

Quinn, T.P. 1993. A review of homing and straying of wild and hatchery-produced salmon. Fisheries Research 18: 29-44.

Reiser, D.W. and T.C. Bjornn. 1979. Habitat requirements of anadromous salmonids. In: W.R. Meehan (ed.), Influence of Forest and Rangeland Management on Anadromous Fish Habitat in the Western United States and Canada. U.S. Department of Agriculture, Forest Service, General Technical Report PNW-96.

Rich, A.A. 1987. Report on studies conducted by Sacramento County to determine the temperatures which optimize growth and survival in juvenile Chinook salmon (Oncorhynchus tshawytscha). Prepared for McDonough, Holland and Allen, Sacramento, California. April 1987. 52 pp + Appendices.

Rich, A.A. 1997. Testimony of Alice A. Rich, Ph.D. Regarding Water Rights Applications for the Delta Wetlands Project, Proposed by Delta Wetlands Properties for Water Storage on Webb Tract, Bacon Island, Boudin Island, and Holland Tract in Contra Costa and San Joaquin counties, Calif.. Dept. Fish and Game Exhibit DFG-7. Submitted to State Water Resource Control Board.

Rich, A.A. and W.E. Loudermilk. 1991. Preliminary evaluation of Chinook salmon smolt quality in the San Joaquin Drainage. Report produced by the Calif. Dept. Fish and Game, Region 4, Fresno, CA. 18 February 1991.

Ricker, W.E. 1972. Hereditary and environmental factors affecting certain salmonids populations. In: R.C. Simon and P.A. Larkin (eds.), The Stock Concept in Pacific Salmon, pp. 19-160. MacMillan Lectures on Fisheries. Univ. British Columbia, Vancouver, B.C.

Ricker, W.E. 1975. Computation and Interpretation of Biological Statistics of Fish Populations. Bulletin 191, Can. Fish. Res. Board, Dept. Environ. Fish. and Marine Sci., Ottawa, Canada. 382 pp.

102


Rondorf, D.W., G.A. Gray, and R.B. Fairley. 1990. Feeding ecology of subyearling Chinook salmon in riverine and reservoir habitats of the Columbia River. Trans. Am. Fish. Soc. 119: 16-24.

Roper, B. and D.L. Scarnecchia. 1996. A comparison of trap efficiencies for wild and hatchery Age-0 Chinook salmon. N. Am. J. Fish. Manage. 16(1):214-217.

Rowell, J.H. 1993. Stanislaus River Basin Model. Draft report produced by the U.S. Bureau of Reclamation, Mid-Pacific Region, Sacramento, CA.

Sagar, P.M. and G.J. Glova. 1988. Diel feeding periodicity, daily ration, and prey selection of a riverine population of juvenile Chinook salmon, Oncorhynchus tshawytshca. J. Fish. Biol. 33: 643-653.

Saiki M.K., M.R. Jennings, and R.H. Wiedmeyer. 1992. Toxicity of agricultural subsurface drainwater from the San Joaquin Valley, California, to juvenile Chinook salmon and striped bass. Trans. Am. Fish. Soc. 121:78–93.

[SJRGA] San Joaquin River Group Authority. 2001. 2000 Annual Technical Report on Implementation and Monitoring of the San Joaquin River Agreement and the Vernalis Adaptive Management Plan. Report prepared for the California State Water Resources Control Board, Sacramento, CA. January 2001.

SJRGA. 2002. 2001 Annual Technical Report on Implementation and Monitoring of the San Joaquin River Agreement and the Vernalis Adaptive Management Plan. Report prepared for the California State Water Resources Control Board, Sacramento, CA. January 2002.

SJRGA. 2003. 2002 Annual Technical Report on Implementation and Monitoring of the San Joaquin River Agreement and the Vernalis Adaptive Management Plan. Report prepared for the California State Water Resources Control Board, Sacramento, CA. January 2003.

Sasaki, S. 1996. Distribution and food habits of king salmon, Oncorhynchus tshawytscha, and steelhead rainbow trout, salmo gairdnerii, in the Sacramento-San Joaquin Delta. Calif. Dept. Fish and Game, Fish Bulletin 133: 108-114.

Sato, G.M. and P.B. Moyle. 1989. Ecology and conservation of spring-run Chinook salmon: Annual report. U.C. Water Resources Center Project W-79, July 30, 1988 – June 30, 1989, Davis, CA.

Saunders, R.L. 1965. Adjustment of buoyancy in young Atlantic salmon and brook trout by changes in swim bladder volume. J. Fish. Res. Bd. Can. 22: 335-352.

Schaffter, R. 2000. Mortality rates of largemouth bass in the Sacramento-San Joaquin Delta, 1980 through 1984. Interagency Ecological Program Newsletter 13(4):54-60.

Seymour, A.H. 1956. Effects of temperature on young Chinook salmon. University of Washington, Seattle, WA.

103


Shapovalov, L., and A.C. Taft. 1954. The life histories of the steelhead rainbow trout (Salmo gairdnerii gairdnerii) and silver salmon (Oncorhynchus kisutch) with special reference to Waddell Creek, California, and recommendations regarding their management. Calif. Dept. Fish and Game, Fish Bulletin 98. 375 pp.

Scholz, N.L., N.K. Truelove, B.L. French, B.A. Berejikian, T.P. Quinn, E. Casillas, and T.K. Collier. 2000. Can. J. Fish. Aquat. Sci. 57: 1911-1918.

Smith, A.K. 1973. Development and application of spawning velocity and depth criteria for Oregon salmonids. Trans. Am. Fish. Soc. 10(2): 312-316.

Smith, L.S. 1982. Decreased swimming performance as a necessary component of the smolt migration in salmon migration in the Columbia River. Aquaculture 28: 153-161.

Sommer, T.R., M.L. Nobriga, W.C. Harrell, W. Batham, and W.J. Kimmerer. 2001a. Floodplain rearing of juvenile Chinook salmon: evidence of enhanced growth and survival. Can. J. Fish. Aquat. Sci. 58: 325-333.

Sommer, T., B. Harrell, M. Nobriga, R. Brown, P. Moyle, W. Kimmerer, and L. Schemel. 2001b. California’s Yolo Bypass: evidence that flood control can be compatible with fisheries, wetlands, wildlife, and agriculture. Fisheries 26: 6-16.

S.P. Cramer and Associates, Inc. 2003. 2003 Stanislaus River Data Report. Final Data Report, S.P. Cramer & Associates, Gresham, Oregon.

[SRFG] Stanislaus River Fish Group. 2003. A plan to restore anadromous fish habitat in the lower Stanislaus River. Draft plan produced by the SRFG for the USFWS Anadromous Fish Restoration Program, Stockton, CA.

[SSR] Off Site Release and Straying Subcommittee. 2001. APPENDIX I. Off Site Release and Straying Subcommittee Report: Report of the subcommittee on off-site release and straying of hatchery produced Chinook salmon available from Internet at http://www.dfg.ca.gov/lands/append1-5.pdf.

Stabler, D.F. 1981. Effects of altered flow regimes, temperatures, and river impoundment on adult steelhead trout and Chinook salmon. M.S. thesis, University of Idaho, Moscow, Idaho. 84 p.

Tabor, R.A., G. Brown, and V.T. Luiting. 1998. The effect of light intensity on predation of sockeye salmon fry by prickly sculpin and torrent sculpin. Prepared by U.S. Fish and Wildlife Service, Western Washington Office, Aquatic Resources Division, Lacey, WA, and U.S. Geological Survey,Western Fisheries Science Center, Seattle, Washington. 16 pp.

Thompson, K. 1972. Determining stream flows for fish life. Proceedings, Instream flow Requirement Workshop. Pacific Northwest Basin Commission, Vancouver, WA.

104

http://www.dfg.ca.gov/lands/append1-5.pdf


[USFWS] U.S. Fish and Wildlife Service. 1995. Working paper on restoration needs: habitat restoration actions to double natural production of anadromous fish in the Central Valley of California, Vol. 2. Prepared for the U.S. Fish and Wildlife Service under the direction of the Anadromous Fish Restoration Program Core Group, Stockton, CA.

Utter, F., G. Milner, G. Stahl, and D. Teel. 1989. Genetic population structure of Chinook salmon (Oncorhynchus tshawytscha), in the Pacific Northwest. Fish. Bull. 87:239-264.

Walters, C.J., R. Hilborn, R.M. Peterman, and M.J. Staley. 1978. Model for examining early ocean limitation of Pacific salmon production. J. Fish. Res. Board Can. 35:1303-1315.

Waters, T.F. 1995. Sediment in streams: sources, biological effects, and control. Am. Fish. Soc. Monograph 7.

Werner, I., L.A. Deanovic, K. Kuivila, J. Orlando, and T. Pedersen. 2003. Concentrations of organophosphate pesticides and corresponding bioassay toxicity in the Sacramento-San Joaquin Delta. Poster presentation at the CALFED Science Conference 2003, Sacramento Convention, Center, January 14-16, 2003. Prepared by the Aquatic Toxicology Program, University of California, Davis and the U.S. Geological Survey, Sacramento.

Workman, M.L. 2002. Lower Mokelumne River upstream fish migration monitoring conducted at Woodbridge Dam August 2001 through July 2002.

Velson, F.P. 1987. Temperature and incubation in Pacific salmon and rainbow trout, a compilation of data on median hatching time, mortality, and embryonic staging. Can. Dept. Fish. Aquat. Sciences. No. 626.

Vogel, D.A. and K.R. Marine. 1995. 1994 biological evaluations of the new fish screen at the Glenn-Colusa Irrigation District’s Sacramento River pump station. Natural Resource Scientists, Inc., Red Bluff, CA. February 1995. 77 pp + appendices.

Yoshiyama, R.M., E.R. Gerstung, F.W. Fisher, and P.B. Moyle. 1996. Historical and present distribution of Chinook salmon in the Central Valley drainage of California. In: Sierra Nevada Ecosystem Project: Final report to Congress, Volume III, pp. 309-362. Centers for Water and Wildland Resources, University of California, Davis, CA.

Zaugg, W.S. and H.H. Wagner. 1973. Gill ATPase activity related to parr-smolt transformation and migration in steelhead trout (Salmo gairdnerii): Influence of photoperiod and temperature. Comp. Biochem. Physiol. 45B:955-965.

Zimmerman, M.P. 1999. Food habits of smallmouth bass, walleyes, and northern pikeminnow in the Lower Columbia River basin during outmigration of juvenile anadromous salmonids. Trans. Am. Fish. Soc. 128:1036-1054.

105


5. PERSONAL COMMUNICATIONS

Cramer, Steve P. Fishery biologist and Principal of S.P. Cramer and Associates, Inc., Gresham, Oregon.

Frymire, P. 2000. Long-term resident of the Stanislaus River corridor, Frymire Road, Knights Ferry, California. Personal communication with Carl Mesick, March 2000.

Guignard, J. 2003. CDFG biologist assigned to the Stanislaus River. La Grange, California. Personal communication with Andrea Fuller, October 2003.

Spada, Tony. CDFG warden. Personal communications with Steve Walser, 2002.

Vogel, Dave. Fishery biologist and principal of Natural Resource Scientists, Red Bluff, California. Personal communication with whom?

Walser, Steve B. Executive Director of California Rivers Restoration Fund and owner/professional fishing guide for Sierra West Adventures, Sonora, California. Personal communication with Carl Mesick, Date?.

Appendix 1 Correlations between Fall-Run Chinook Salmon Recruitment to the Lower Stanislaus River and Stock, Streamflow, and Delta Exports from 1950 to 2002

Appendix 2 Gravel Mining and Scour of Salmonid Spawning Habitat in the Lower Stanislaus

River

Appendix 3 Water Temperature at Vernalis during Spring Relative to Streamflow

106


Need date.


With whom?


With whom and when?

Documents

I€¦ · Web viewA Summary of Fisheries Research In The Lower Stanislaus River. Screw trap used to catch juvenile salmonids near Oakdale. Stanislaus River Fish Group