Atlantic Salmon Smolt Migration and Survival Prior to Dam Removal

The effects of dams on Atlantic salmon smolt migration and survival were studied in the Penobscot River, Maine to develop baseline knowledge prior to the removal of two dams in the river. Wild (n=417) and hatchery (n=1228) Atlantic salmon smolts were acoustically tagged and released at multiple locations in the river 2005-2011.  Smolts were detected throughout the river and estuary during migration using an array of acoustic receivers.  Movement rates and passage path of fish were characterized in impounded and free-flowing sections of the Penobscot River.  Survival was estimated in various reaches of the river each year using multi-state, Cormack-Jolly-Seber (CJS) mark-recapture models that included path choice through a secondary migratory route in fresh water (Stillwater Branch).  We present a comprehensive model of Atlantic salmon smolt survival through freshwater in the Penobscot River based on CJS models.  Reach-specific movement rates and survival probabilities of Atlantic salmon smolts were higher in free-flowing reaches of the river than in impoundments.  Most acoustically tagged smolts (~80%) migrated through main stem of the Penobscot River in all years, and not the Stillwater Branch.  Atlantic salmon smolt survival varied between reaches each year, and generally was higher in free-flowing river reaches than in impounded reaches.