We examined a 36-year record of concurrent midwater trawl and water quality sampling conducted during fall to evaluate habitat trends for three declining fish species in the San Francisco Estuary, California, USA: delta smelt (Hypomesus transpacificus), striped bass (Morone saxatilis), and threadfin shad (Dorosoma petenense). Generalized additive modeling revealed that Secchi depth and specific conductance were important predictors of occurrence for delta smelt and striped bass, while specific conductance and water temperature were important for threadfin shad. Habitat suitability derived from model predictions exhibited significant long-term declines for each species; the southeastern and western regions of the estuary exhibited the most dramatic changes. Declines in habitat suitability were associated with anthropogenic modifications to the ecosystem. For delta smelt, an imperiled annual species endemic to the estuary, the combined effects of fall stock abundance and water quality predicted recruit abundance during recent years of chronically low food supply. Our results are consistent with existing evidence of a long-term decline in carrying capacity for delta smelt and striped bass and demonstrate the utility of long-term data sets for evaluating relationships between fish and their habitat.

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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.

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In this study, we provide evidence that the Yolo Bypass, the primary floodplain of the lower Sacramento River (California, U.S.A.), provides better rearing and migration habitat for juvenile chinook salmon (Oncorhynchus tshawytscha) than adjacent river channels. During 1998 and 1999, salmon increased in size substantially faster in the seasonally inundated agricultural floodplain than in the river, suggesting better growth rates. Similarly, coded-wiretagged juveniles released in the floodplain were significantly larger at recapture and had higher apparent growth rates than those concurrently released in the river. Improved growth rates in the floodplain were in part a result of significantly higher prey consumption, reflecting greater availability of drift invertebrates. Bioenergetic modeling suggested that feeding success was greater in the floodplain than in the river, despite increased metabolic costs of rearing in the significantly warmer floodplain. Survival indices for coded-wire-tagged groups were somewhat higher for those released in the floodplain than for those released in the river, but the differences were not statistically significant. Growth, survival, feeding success, and prey availability were higher in 1998 than in 1999, a year in which flow was more moderate, indicating that hydrology affects the quality of floodplain rearing habitat. These findings support the predictions of the flood pulse concept and provide new insight into the importance of the floodplain for salmon.Résumé : Notre étude démontre que le canal de dérivation Yolo, la principale plaine d'inondation de la région aval de la rivière Sacramento (Californie, É.-U.), offre de meilleurs habitats pour l'alevinage et la migration des jeunes Saumons Quinnat (Onchorhynchus tshawytscha) que les bras adjacents de la rivière. En 1998 et 1999, la taille des saumons a augmenté plus rapidement dans la plaine d'inondation agricole, sujette aux débordements saisonniers de crue, que dans la rivière, ce qui laisse croire à de meilleurs taux de croissance. De plus, des jeunes saumons marqués à l'aide de fils de métal codés et relâchés dans la plaine d'inondation étaient plus gros au moment de leur recapture et avaient des taux de croissance apparente plus élevés que des poissons relâchés dans la rivière en même temps. L'amélioration des taux de croissance dans la plaine de débordement résultait en partie d'une consommation significativement plus importante de proies, le reflet d'une plus grande disponibilité des invertébrés de la dérive. Un modèle bioénergétique laisse croire que le succès de l'alimentation a été meilleur dans la plaine d'inondation que dans la rivière, en dépit du coût métabolique d'alevinage significativement plus grand dans les eaux plus chaudes de la plaine d'inondation. Les indices de survie des poissons marqués et relâchés dans la plaine d'inondation étaient quelque peu plus élevés que ceux des poissons de la rivière, mais les différences n'étaient pas statistiquement significatives. La croissance, la survie, le succès de l'al...

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