Abstract.-We examined factors affecting fish entrainment at California's State Water Project and Central Valley Project, two of the largest water diversions in the world. Combined, these diversions from the upper San Francisco Estuary support a large component of the municipal and agricultural infrastructure for California. However, precipitous declines in the abundance of several estuarine fish species, notably the threatened delta smelt Hypomesus transpacificus, have generated major concern about entrainment as a possible cause of the declines. We examined a 13-year data set of export pumping operations and environmental characteristics to determine factors affecting entrainment (as indexed by salvage at fish screens) and the potential for manipulation of these factors to improve conditions for fish. Entrainment of three migratory pelagic species-delta smelt, longfin smelt Spirinchus thaleichthys, and striped bass Morone saxatilis-was primarily determined by the seasonal occurrence of particular life stages close to the export facilities. We also found that the direction and magnitude of flows through the estuary and to the export facilities were reasonable predictors of pelagic fish entrainment. Entrainment of resident demersal species (prickly sculpin Cottus asper and white catfish Ameiurus catus) and littoral species (Mississippi silverside Menidia audens and largemouth bass Micropterus salmoides) was not explained by diversion flows, although large numbers of individuals from these species were collected. Our study suggests that entrainment of pelagic species can be effectively reduced by manipulating system hydrodynamics.

No abstract

The biomass of fish populations is often calculated from abundance-by-length data using length-weight (LW) relationships from separate studies (e.g., from the literature). Estimates of biomass determined this way have two principal sources of error: (1) error in total numbers and size distribution of fish due to sampling variability; and (2) prediction error, including that arising from the use of a LW relationship from another time, place, population, or species. We developed LW relationships from 6,390 measurements of fish of 24 species in the San Francisco Estuary. Our principal objective was to evaluate the errors that arise when calculating biomass from length data. Data were obtained from four sampling studies (none designed for this purpose) and analyzed with analysis of covariance on log-transformed data. Differences in LW relationships among studies were apparent. Five tests were applied to assess the influence of these differences on predictions of biomass from length data. Three of these tests indicated some bias arising from several sources, including differences in the range of lengths used to develop the relationships. The remaining two tests compared the sampling variability of two common fish species with variability and bias introduced by means of different alternative LW relationships from our data and from the literature. Length-weight relationships from the literature introduced some bias and somewhat more variability into the biomass estimates compared with estimates based on LW relationships obtained from the San Francisco Estuary. However, sampling error was the largest source of error in all cases. Although it is preferable to calculate biomass from LW relationships of fish from the same area and time period, the error induced by using relationships from other time periods, other areas, or the literature is typically small compared with sampling error, particularly when only relative measures of biomass are needed.

While there is substantial information about the upstream migration of commercially and recreationally important fishes, relatively little is known about the upstream migration of small-bodied species, particularly through estuaries. In the San Francisco Estuary, there is a major need to understand the behavior of delta smelt Hypomesus transpacificus, a small pelagic fish listed under the state and federal endangered species acts. The spawning migration period may be critical as upstream movements can result in entrainment in water diversions. In general, delta smelt live in the low-salinity zone of the estuary and migrate upstream for spawning. During the fall pre-migration period, delta smelt remain primarily within the low-salinity zone in the western Sacramento-San Joaquin Delta and Suisun Bay. There were no significant upstream shifts of fish into fresher water during late fall, suggesting that delta smelt do not show pre-migration staging behavior. Following winter "first flush" flow events that appear to trigger migration, upstream movement rates are relatively rapid, averaging 3.6 km d -1 , a finding consistent with results from particle-tracking simulations, laboratory studies, and other fishes. Like some other native fishes, delta smelt apparently "hold" in upstream areas following migration; most do not spawn immediately. Overall, delta smelt fit the pattern of a diadromous species that is a seasonal reproductive migrant. Emerging data suggest that there is variability in the migration behavior of delta smelt, a pattern contrary to the reigning viewpoint that all smelt migrate in winter.

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While there is substantial information about the upstream migration of commercially and recreationally important fishes, relatively little is known about the upstream migration of small-bodied species, particularly through estuaries. In the San Francisco Estuary, there is a major need to understand the behavior of delta smelt Hypomesus transpacificus, a small pelagic fish listed under the state and federal endangered species acts. The spawning migration period may be critical as upstream movements can result in entrainment in water diversions. In general, delta smelt live in the low-salinity zone of the estuary and migrate upstream for spawning. During the fall pre-migration period, delta smelt remain primarily within the low-salinity zone in the western Sacramento-San Joaquin Delta and Suisun Bay. There were no significant upstream shifts of fish into fresher water during late fall, suggesting that delta smelt do not show pre-migration staging behavior. Following winter "first flush" flow events that appear to trigger migration, upstream movement rates are relatively rapid, averaging 3.6 km d -1 , a finding consistent with results from particle-tracking simulations, laboratory studies, and other fishes. Like some other native fishes, delta smelt apparently "hold" in upstream areas following migration; most do not spawn immediately. Overall, delta smelt fit the pattern of a diadromous species that is a seasonal reproductive migrant. Emerging data suggest that there is variability in the migration behavior of delta smelt, a pattern contrary to the reigning viewpoint that all smelt migrate in winter.

Estuarine food webs are highly variable and complex, making identification of their trophic pathways difficult. Energy for the food web of the San Francisco Estuary is thought to be based largely on in situ phytoplankton production, but little attention has been paid to littoral habitats, where other energy sources may be important. We analyzed the stomach contents of over 960 juvenile fishes and the stable carbon and nitrogen isotope ratios of these fishes and their potential food resources in pelagic and littoral habitats from the tidal freshwater area of the estuary. The mixing model IsoSource was used to examine energy sources important to consumers. Our results show evidence of two predominant food web pathways. Pelagic fishes and some littoral fishes showed strong dependence on a zooplankton–phytoplankton trophic pathway. However, the majority of fishes in littoral habitats had diets and carbon isotope ratios consistent with energy arising from submerged aquatic vegetation and epiphytic macroalgae. IsoSource revealed that the overall majority of nutrition of littoral fishes originated from consumption of grazer amphipods. Examining both stable isotopes and stomach contents allowed us to identify a food web with contributions to resident fishes that had been previously underestimated in the estuary. This study provides insight to how estuarine food webs have changed over the last few decades and highlights why the functions of habitats must be understood for effective restoration planning.

Recruitment of estuarine organisms can vary dramatically from year to year with abiotic and biotic conditions. The San Francisco Estuary (California, USA) supports a dynamic ecosystem that receives freshwater flow from numerous tributaries that drain one of the largest watersheds in western North America. In this study, we examined distribution and habitat use of two forage fish larvae of management interest, Longfin Smelt Spirinchus thaleichthys and Pacific Herring Clupea pallasii, during a low-flow and a high-flow year to better understand how their rearing locations (region and habitat) may affect their annual recruitment variability. During the low-flow year, larval and post-larval Longfin Smelt were distributed landward, where suitable salinity overlapped with spawning habitats. During the high-flow year, larval Longfin Smelt were distributed seaward, with many collected in smaller tributaries and shallow habitats of San Francisco Bay. Local spawning and advection from seaward habitats were speculated to be the primary mechanisms that underlie larval Longfin Smelt distribution during the high-flow year. Larval Pacific Herring were more abundant seaward in both years, but a modest number of larvae were also found landward during the low-flow year. Larval Pacific Herring abundance was lower overall in the high-flow year, suggesting advection out of the area or poor recruitment. Future monitoring and conservation efforts for Longfin Smelt and Pacific Herring should recognize that potential mechanisms underlying their recruitment can vary broadly across the San Francisco Estuary in any given year, which suggests that monitoring and research of these two species expand accordingly with hydrologic conditions that are likely to affect their spawning and larval rearing distributions.