California Department of Fish and Wildlife

Fish Bulletin 179 - Contributions to the Biology of Central Valley Salmonids, Volume 2 of 2

Title: Contributions to the Biology of Central Valley Salmonids, Volume 2 (PDF)
Description: The Salmonid Symposium was organized by an ad hoc committee of state and federal fishery biologists concerned with the management of Central Valley (CV) salmon and steelhead trout (Oncorhynchus spp.) populations and their habitats. It was held at Bodega Bay , California on October 22–24, 1997 . Topics covered included research on various CV salmon and steelhead populations, ocean fishery management, history of upper Sacramento River hatchery operations, and steelhead management policy.
Editor: Randall L. Brown, Department of Water Resources
Pages: 378
Published: 2001

Download Individual Papers

  • Title: Front Matter (PDF)
    Description: Consists of Title page, copyright, table of contents, preface, dedication, in appreciation, acknowledgements, foreward, contributing authors pages.
    Editor: Randall L. Brown, Department of Water Resources
  • Title: Chinook Salmon in the Lower American River, California's Largest Urban Stream (PDF)
    Abstract: The American River now supports a mixed run of hatchery and naturally- produced fall-run chinook averaging about 30,000 spawners; the spring-run was lost to dams. Salmon in the river have been much studied over the last 20 years, largely because of litigation over proposed diversions, but much uncertainty remains about various aspects of their biology and about the environmental conditions needed to support them. This paper briefly reviews what is known and not known about salmon in the American River and makes recommendations for future work.
    Author: John G. Williams
  • Title: Juvenile Chinook Salmon Abundance, Distribution, and Survival in the Sacramento-San Joaquin Estuary (PDF)
    Abstract: All four races of juvenile Central Valley chinook salmon migrate through and many rear in the Sacramento-San Joaquin Delta and Estuary. Delta residence and migration is considered important in determining adult production, as it is generally believed that density dependent effects are minimal after this life stage. Populations of winter run and spring run are presently listed as endangered and threatened species, while the remaining populations in the Central Valley are candidate species. Actions in the Delta to improve survival are likely important in the recovery of these depressed populations. The tidally influenced freshwater Delta also is an important area for water management in California , as it is where the Central Valley and State Water Project pump large volumes of water to southern California , the San Joaquin Valley and the Bay area. To document the effect of these various water management activities in the Delta on juvenile salmon, monitoring and special studies have been conducted since the early 1970s to the present. Changes in abundance in the Delta and estuary appear related to flow; high flows increase the use of the Delta and San Francisco Bay by fry. Relative survival of fry appears greater in the upper Sacramento River than in the Delta or bay, especially in the wetter years. Survival appears lower in the Central Delta relative to that in the North Delta in drier years for both fry and smolts. Fall-run smolt and late-fall-run yearling survival studies have found that diversion into the Central Delta via the Delta Cross Channel or Georgiana Slough reduces survival through the Delta. Experiments in the San Joaquin Delta have shown that survival appears greater for smolts that migrate down the mainstem San Joaquin River rather than through upper Old River . A temporary barrier in upper Old River was tested and found to improve survival for smolts originating in the San Joaquin basin. These specific experiments have identified management actions that could improve juvenile salmon survival through the Delta. In addition, indices of annual survival provide a way to compare survival through the Delta and could be used to assess restoration and management actions. This work demonstrates how long-term scientific studies can be applied to address management and restoration issues.
    Author: Patricia L. Brandes and Jeffrey S. McLain
  • Title: The Effects of San Joaquin River Flows and Delta Export Rates During October on the Number of Adult San Joaquin Chinook Salmon that Stray (PDF)
    Abstract: This report describes a two-part investigation of the effects of fall make-up pumping on straying of adult San Joaquin chinook salmon. The first part is a reevaluation of 1964 to 1967 data collected by Hallock and others (1970) on the migratory behavior of tagged and untagged adult San Joaquin salmon in the Delta. The second part is an evaluation of the recovery of adult salmon that were released in the San Joaquin basin as coded-wire tagged juveniles reared at the Merced River Fish Facility.
    There are three important results from Hallock and others (1970) regarding their migration analysis. First, adult salmon are migrating through the San Joaquin Delta near Prisoners Point primarily during October, the period when they are probably most susceptible to low flows and high exports. Second, the fish migrate slowly and do not arrive in the San Joaquin tributaries until about four weeks after they pass Prisoners Point, even when flows, exports, and dissolved oxygen concentrations near Stockton are suitable for migration. And third, migration rates of adult salmon are substantially higher when Vernalis flows exceed about 3,000 cfs and total exports are less than 100% of Vernalis flows. Although most of the tagged fish migrated into the Sacramento and Mokelumne basins when Vernalis flows were less than about 2,000 cfs and total exports exceeded 150% of Vernalis flows, there is uncertainty as to whether these were San Joaquin fish that strayed or Sacramento River fish that were captured in the San Joaquin on their way to the Sacramento River.
    The coded-wire-tag (CWT) recovery data may not have been appropriate for a straying analysis because there are no clear records of the number of fish examined for tags during the carcass surveys. Not all fish counted for the carcass survey were examined for tags. These recovery data are necessary to accurately compute the total number of adult salmon with tags in each river. A casual inspection of the CWT recovery data suggests that: (1) straying rates increased as the percentage of San Joaquin flow exported by the CVP and SWP pumping facilities increased and (2) the critical period is between 1 and 21 October. Furthermore, pulse flows from the San Joaquin tributaries, or a reduction of Delta exports that result in no more than a 300% export rate of San Joaquin flows at Vernalis for eight to twelve days in mid-October, are sufficient to keep straying rates below 3%.
    The results of these correlation analyses suggest that when more than 300% of Vernalis flow is exported over a ten-day period in mid-October adult San Joaquin chinook salmon stray to the Sacramento and eastside basins. However, further tests are needed due to the limitations of the existing data.
    Author: Carl Mesick
  • Title: Survival of Chinook Salmon Smolts in the Sacramento-San Joaquin Delta and Pacific Ocean (PDF)
    Abstract: This paper summarizes current knowledge about the effects of river flow and water export on the survival of San Joaquin River Basin chinook salmon smolts migrating through the Sacramento-San Joaquin Delta. As will become clear, there are serious deficiencies in our understanding of the needs of smolts as they pass through this region, but there is a general agreement that mortality can be high and can probably be reduced by management actions. The potential for success of the various alternatives remains speculative; something needs to be done, but it remains unclear what will work best. For example, smolt survival is usually better at very high (flood) flows than at very low flows, but there is little solid information about the potential for improved survival in the range that might be managed regularly. Researchers have not really begun the search for optimal flows for smolt survival; analyses to date offer, at best, only the qualitative guidance that “higher” flows are “better” for salmon, without any indication of just how much better survival can be or should be. Similarly, although there is reason to believe that strategically placed barriers should improve smolt survival, by keeping smolts well away from the Delta export pumps; however, experiments to date have not been able to demonstrate or refute the effectiveness of such barriers directly.
    Author: Peter F. Baker and J. Emil Morhardt
  • Title: Ocean Salmon Fishery Management (PDF)
    Abstract: California ocean salmon fisheries are managed by the Pacific Fishery Management Council (Council) under the federal Magnuson-Stevens Fishery Conservation and Management Act. This chapter describes the ocean fisheries impacting California Central Valley (CV) chinook stocks, the federal regulatory process that is followed in managing these ocean fisheries, and discusses alternative management measures for protecting valuable natural resources. The CV supports fall, late-fall, winter, and spring chinook runs. The Council has adopted a spawning escapement goal for the fall run, while a federal rebuilding plan is used to regulate the fisheries to protect the winter run, an endangered species. The winter run plan is also protective of CV spring run, a threatened species. Some potential alternative management strategies include (1) a revised escapement goal for the Sacramento fall run, (2) a separate escapement goal for the spring run, (3) an escapement goal for the San Joaquin fall run, and (4) a selective ocean fishery for marked hatchery fish. The CV salmon management program is lacking in two areas: (1) river return estimates for codedwire- tagged fish releases and (2) inconsistent tagging of hatchery fish releases, precluding estimation of hatchery fish contributions. I conclude that a comprehensive fishery management program should be implemented for CV chinook salmon under the Central Valley Project Improvement Act and that the Klamath Fishery Management Council be used as a model for developing such a program.
    Author: L.B. Boydstun
  • Title: Population Trends and Escapement Estimation of Mokelumne River Fall-run Chinook Salmon (Oncorhynchus tshawytscha) (PDF)
    Abstract: In 1990 the East Bay Municipal Utility District (EBMUD) began a program to monitor the fall-run chinook salmon (Oncorhynchus tshawytscha) populations in the lower Mokelumne River using video and trapping at Woodbridge Dam and weekly redd surveys.
    Over the eight years of this monitoring program, the Mokelumne River fall-run chinook salmon escapement showed a trend of increased abundance of both hatchery and natural spawners. The 1997 estimated total spawning escapement (combined hatchery and natural run) was 10,175 compared to a spawning escapement of 497 in 1990 and the 57-year average escapement of 3,434 fish. The estimated natural spawning population fluctuated from a low of 369 in 1991 to a high of 3,892 fish (1,739.3 ± 1,384.9) in 1996. The percentage of natural spawners ranged between 31% to 90% (52.3 ± 19.9) of the total spawning escapement during the 1991–1997 period.
    Significant correlations were observed between the number of redds and total escapement ( R² = 0.941, P < 0.0001) and the hatchery returns and total spawning escapement ( R² = 0.972, P < 0.001). The later correlation was used to determine the accuracy of past spawning escapement estimates based upon a similar correlation using a narrower dataset.
    These results suggest accurate total spawning escapement estimates can be obtained from hatchery returns and from redd counts. Escapement estimates calculated from redd counts and compared with known estimates were accurate in the mid-range while those calculated from hatchery returns were accurate throughout the range of run sizes.
    Author: Joseph J. Miyamoto and Roger D. Hartwell
  • Title: Studies of Spawning Habitat for Fall-Run Chinook Salmon in the Stanislaus River Between Goodwin Dam and Riverbank from 1994 to 1997 (PDF)
    Abstract: The spawning habitat of fall-run chinook salmon (Oncorhynchus tshawytscha) was studied in the Stanislaus River between Goodwin Dam and Riverbank between 1994 and 1997 to evaluate whether habitat quality was potentially limiting the population and whether two restoration projects improved spawning conditions. Redd surveys in 1994 and 1995 indicated that spawning was concentrated in the riffles located in the 12-mile reach between Goodwin Dam and Orange Blossom Bridge . Most of the spawning (73%) occurred upstream of the riffles' crests where the streambed gradient was positive (for example, the tail of a pool). Sample areas were divided into the upper, middle, and lower portions of riffles to determine why the salmon used the upper areas.
    Substrate samples collected from the upper six inches of the streambed indicated that predicted survival probabilities for chinook salmon eggs using Tappel and Bjornn's (1983) laboratory study averaged 75.6% in the reach above the Orange Blossom Bridge, 58.6% in the lower spawning reach between the bridge and town of Riverbank, and 95.4% at two restoration sites near the U.S. Army Corps of Engineers' Horseshoe Road park where gravel was added in 1994. Predicted egg survival probabilities averaged 73.2% upstream of riffle crests and 62.1% downstream of riffle crests at four natural riffles with pronounced crests.
    Intragravel dissolved oxygen (DO) concentrations were relatively constant at 32 piezometer sites in the 12 study riffles during five surveys conducted at 10-day intervals in November and December 1995. The DO levels declined markedly in early February 1996 at nine sites shortly after runoff from four major storms increased base flows from 300 cfs to as much as 800 cfs for several days after each storm. Prior to the storms in November and December, intragravel DO concentrations were less than 5 ppm at six piezometer sites (19%) and less than 8 ppm at eleven sites (34%). Immediately after the fifth major storm in early February, intragravel DO concentrations were less than 5 ppm 218 Fish Bulletin 179: Volume Two at 11 piezometer sites and less than 8 ppm at 16 sites (50%). Many of the sites where DO concentrations were low were associated with intragravel water temperatures that were between 1° and 6° F higher than surface temperatures. The elevated temperatures suggest the inflow of oxygen-poor groundwater. A high rate of groundwater inflow into the Stanislaus River 's riffles would explain the unexpectedly positive vertical hydraulic gradients upstream of the riffle crests measured at most of the piezometer sites in fall 1996.
    A regression model of the average intragravel DO concentrations in November and December 1995 had an adj- R² of 0.80 with significant ( P ≤ 0.05) variables that include an index of groundwater inflow, abundance of Asian clams (Corbicula fluminea), percent fines <2 mm, and mean column water velocity. A model for the February 1996 DO concentrations had an adj- R² of 0.68 with significant variables that include the groundwater index and the percent fines <2 mm. Although streambed gradient indexes were not selected for the regression models, DO concentrations that were greater than 80% saturation in February 1996 usually occurred where the gradient was positive 2% or higher.
    Not all restoration sites in the Stanislaus River where clean gravel was added were used by spawning salmon. Two riffles constructed with imported gravel from the Merced River were used by very few fish for three years even though intragravel DO levels were near saturation and spawning occurred in the immediate vicinity. After high flows deposited a large berm of native rock at the crest of one of these riffles in spring 1997, a relatively high number of salmon began spawning in the new substrate in fall 1997. In Goodwin Canyon , where gravel was lacking, many salmon quickly spawned in newly added gravel from the Stanislaus' floodplain placed in late summer 1997.
    Author: Carl Mesick
  • Title: Distribution and Abundance of Chinook Salmon and Resident Fishes of the Lower Tuolumne River, California (PDF)
    Abstract: The Tuolumne River chinook salmon (Oncorhynchus tshawytscha) population represents one of the southernmost populations of the species and is of considerable management interest. This paper compiles and analyzes data available through 1997 for chinook salmon and other fish species occurring in the lower Tuolumne River. Estimates of adult fall-run chinook salmon varied from about 100 to 130,000 from 1940 to 1997 (mean: 18,300; median: 7,100). Age composition varied widely from 1981 to 1997; however, three-year-old fish usually dominated the population. The percentage of females in the population varied from 25% to 67% during 1971–1997. The percentage of tagged adult salmon increased from less than 2% before 1987 to an average of 20% during 1992–1997. Density of juvenile chinook salmon generally declined each year after a winter peak in fry abundance. Average, minimum, and maximum fork length of juvenile chinook salmon typically increased after February; although, declines occurred in some years because of large captures of fry in late spring. Few juvenile chinook salmon resided in the river over the summer during 1988–1993. A total of 33 taxa of fish (12 native and 21 introduced), including chinook salmon, was captured during various sampling programs. Native species were most frequent in upstream areas above river kilometer (rkm) 80. Introduced species dominated areas downstream of rkm 50. The resident fish community appeared to vary in response to annual differences in flow conditions with native species becoming more abundant in the year following a high flow year. There was no discernible seasonal change in fish communities when early summer (early June) and late summer (mid September) samples from the same sites were compared. Monitoring of the Tuolumne River chinook salmon population has provided valuable data on both chinook salmon and populations of other fish species.
    Author: Tim Ford and Larry R. Brown
  • Title: Building Models and Gathering Data: Can We Do This Better? (PDF)
    Abstract: We are constructing a “second generation” model of chinook salmon for the Sacramento Basin to help investigate factors affecting salmon populations and the effects of management actions. We chose to build a new model rather than modify an older one to apply recent developments in computer interfaces and individual-based modeling and to incorporate a more detailed and flexible geographic representation. We also expected that substantial new knowledge had been developed that would enable us better to characterize the life cycle and influences on survival of chinook salmon. These expectations have not been met, and despite some recent progress we still find gaps between the knowledge available and that needed for successful modeling. Key examples of gaps in our knowledge include sublethal temperature effects, abundance of young fish, factors triggering migration, factors limiting rearing habitat, and survival of young salmon, particularly fry rearing in the mainstem or Delta reaches and early survival in the ocean. We believe these gaps arise for several reasons: (1) a mismatch in perceptions of what data are needed; (2) a lack of institutional commitment to long-term, broad-scale programs to provide knowledge useful in modeling; and (3) the fundamental difficulty of gathering information about environmental influences on fish populations.
    Author: Wim Kimmerer, Bill Mitchell, and Andy Hamilton
  • Title: Exploring the Role of Captive Broodstock Programs in Salmon Restoration (PDF)
    Abstract: Severe population declines have occurred in many Pacific salmon stocks. Stock declines have been attributed to both anthropogenic and natural environmental causes. These declines have been so dramatic that resource agencies have not had the time or means to quantitatively describe stocks and develop rapid, reliable methods of conserving rare genes. One method to prevent extinction is gene banking by means of rearing broodstock in captivity for use in supplementing rare and endangered stocks. With varying degrees of success, several captive breeding programs have been initiated to provide “insurance” against genetic loss of imperiled stocks. Captive breeding is expensive, requiring long-term intensive fish husbandry. It is not an alternative to habitat restoration. In certain situations, such as small runs (20 to 100 spawning adults) combined with habitat undergoing restoration, captive breeding may be a desirable supplementation strategy. It is certainly a beneficial option for any stock on the edge of extinction. There are several salmon captive broodstock programs on the west coast of North America , each employing different approaches and technologies. Captive breeding techniques are evolved to a point where the progeny of wild fish can be reared with a high degree of success. However, this kind of intervention is costly and must be weighed against other factors that will determine stock recovery. It is incumbent upon managers and scientists to define the uncertainty, or risk, of captive breeding. Risk assessment is an essential component of any captive breeding program. Emerging captive breeding programs can benefit from the range of experience and technological development that has evolved over the past decade. Molecular genetics, captive broodstock technology, conservation biology, and fisheries supplementation risk assessment have matured to a stage where salmonid captive breeding can be planned as an intervention with a measured effect.
    Author: Kristen D. Arkush and Paul A. Siri
  • Title: Are Juvenile Chinook Salmon Entrained at Unscreened Diversions in Direct Proportion to the Volume of Water Diverted? (PDF)
    Abstract: Mark-recapture experiments were used to test the null hypothesis that juvenile chinook salmon smolts emigrating from the Sacramento River are entrained at unscreened water diversions in direct proportion to the water volume diverted. The experiments were conducted at the RD1004 Princeton Pumping Plant during June 1995, with a similar set of mark-recapture experiments conducted at the RD108 Wilkins Slough diversion. Results of four tests conducted at the RD1004 Princeton Pumping Plant showed an average of 0.05% of the marked salmon being entrained, compared to 1.03% of the Sacramento River flow diverted. Overall results at the RD108 Wilkins Slough diversion showed a similar pattern, with 0.08% of the marked salmon being recaptured compared to 1.1% of the Sacramento River flow being diverted. Based upon results of these tests the null hypothesis was rejected. The percentage of juvenile chinook salmon entrained was more than ten times lower than the corresponding percentage of Sacramento River flow diverted. Results of these tests have implications in the assessment of entrainment mortality of juvenile chinook salmon at unscreened diversions and the calculation of costs and biological benefits for intake screening projects. These study results are limited, however, due to the relatively low percentage of Sacramento River flow diverted during these 1995 tests, the assumption that hatchery-reared, spray-dyed salmon released a relatively short distance upstream of an unscreened diversion are representative of the behavioral patterns and distribution of wild salmon within the Sacramento River, and the size and configuration of water diversions tested.
    Author: Charles H. Hanson
  • Title: Inventory of Water Diversions in Four Geographic Areas in California's Central Valley (PDF)
    Abstract: Water diversions in California , used primarily for agricultural, municipal, and industrial applications, have been considered a possible culprit in the decline of many California fishes. In 1991, the California Department of Fish and Game (DFG) initiated a study using the Global Positioning System (GPS) to inventory water diversions. The initial focus was on the Sacramento-San Joaquin Delta (Delta) and the Suisun Marsh, then continued to the Sacramento River and the San Joaquin River Basin, The inventory was to find, quantify, describe, and categorize diversions along waterways where California fish may be affected by water diversions. As of April 1997, 3,356 diversions have been located and mapped in a Geographical Information System (GIS). Approximately 98.5% of the diversions identified were either unscreened or screened insufficiently to prevent fish entrainment. The GPS data were post-processed to provide a horizontal accuracy of ±5 meters. The information was primarily collected by visual inspection of diversions on the stream bank. Information is maintained in a Microsoft Access database.
    Author: Janna R. Herren and Spencer S. Kawasaki