Hatchery Influence on Stock Composition, Habitat Use, and Life History Expression By Juvenile Chinook Salmon Oncorhynchus tshawytscha in the Columbia River Estuary

The Columbia River is an example of a large basin where salmon populations are managed simultaneously for phenotypic simplicity (through hatchery production to mitigate for habitat loss) and phenotypic complexity (through habitat restoration to enhance life history expression and survival).  We synthesized recent survey data to evaluate effects of this dual management approach on juvenile Chinook salmon in the estuary. The results indicate that the estuarine life histories of most Chinook are now driven by hatchery programs.  Hatchery releases determine salmon abundance patterns, stock composition, and size distributions in the estuary. On average hatchery Chinook enter the estuary at larger sizes, seek deeper channel habitats further from shore, concentrate nearer the river mouth, and migrate faster than many smaller, naturally-produced juveniles. Nonetheless, releases from scores of upriver facilities create a protracted estuary migration of hatchery juveniles that overlaps with naturally-produced Chinook, even in shallow habitats. Recent comprehensive hatchery reforms designed to integrate or segregate hatchery and wild stocks in natal streams do not account for interactions in the estuary.  Our survey results raise questions about the ecological responses to concentrated pulses of similarly-sized hatchery fish and the effectiveness of habitat restoration in an estuary dominated by large hatchery phenotypes.