San Francisco Estuary and Watershed Science

Central Valley Chinook must pass through the San Francisco Estuary as juveniles and again as maturing adults. Much attention has been given to the effects on Chinook of management of the freshwater part of the estuary, and the Sacramento–San Joaquin Delta, and especially to the effects on Chinook of diversions of water from the Delta. Here, I review available information on juvenile Chinook in and around the estuary that seems most relevant to management of the estuary and of Chinook. Most naturally produced juvenile fall Chinook enter the estuary as small fish (<50 mm) that typically use tidal habitats, and anthropogenic changes in the Delta and around the bays have sharply reduced that habitat. Nevertheless, there is evidence that many surviving naturally produced fall Chinook leave fresh water at <55 mm length. Juvenile Chinook from other runs are older and larger when they enter the estuary, and probably pass through it more rapidly. Presumably, these have been less directly affected by loss of tidal habitat, but are also affected by degradation of the estuarine ecosystem. The effects of Delta diversions on Chinook vary strongly by run and river of origin; surprisingly few Sacramento River fall Chinook have been recovered at the diversions. Central Valley Chinook, especially fall Chinook, are strongly affected by hatchery culture that reduces juvenile life-history diversity, probably results in density-dependent mortality in the estuary, and presumably reduces fitness for natural reproduction. Hatchery culture diverts juvenile fall Chinook away from, and precludes for selection for, the life history trajectories followed by most naturally produced fish, to which more attention should be given.