Atlantic salmon (Salmo salar) smolts of wild and hatchery origins (n = 522) were tagged with ultrasonic transmitters and monitored at successive arrays of submerged receivers during migration from five watersheds in three regions of the Bay of Fundy (BoF), Canada. Two of the regions had endangered inner BoF salmon populations. Migration success of postsmolts leaving the BoF varied widely among 13 groups monitored (3%-70%) and was influenced by behaviour and passage time. Region of origin was the key variable in habitat-specific survival models selected using the Akaike information criterion. Rearing origin, migration and release timing, and smolt size were important variables in some habitats. Estimated survival rates (overall and habitat specific) differed markedly among salmon populations of different regions. Mediocre estuarine survival of smolts (0.54) from the outer BoF region affected overall survival (0.66), Poor survival (0.21) in coastal areas of the distant inner BoF region and mediocre survival in other habitats resulted in low overall survival (0.06) that severely limited the potential for population recovery. Potential predators were abundant in habitats where survival was lowest. High survival of salmon from the intermediate inner BoF region in all habitats (0.81-0.93) was not responsible for their failure to return.
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