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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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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