Historic drought influences outmigration dynamics of juvenile fall and spring-run Chinook Salmon

Riverine ecosystems around the world have undergone extensive anthropogenic alterations, often to the detriment of native aquatic biodiversity. Migratory fishes are particularly vulnerable to habitat fragmentation and degradation. For example, Chinook Salmon populations in the Sacramento River, CA have been declining for nearly a century. Its Mediterranean climate, position in a landscape dominated by urban and agricultural land use, and the presence of an inland delta that serves as the hub of California's vast water conveyance system, makes this a particularly perilous region for migrating juvenile salmon. This study used acoustic telemetry to investigate survival and routing of juvenile fall and spring-run Chinook Salmon through their riverine and estuarine migratory phases during the historic California drought of 2012-2016. Survival to the ocean in this river system is already lower relative to Chinook Salmon populations in North American. Survival to the Pacific Ocean ranged from 0.0-9.1% over the course of this three-year study. Use of four migratory routes through the Delta was variable, both within and between years. We documented extensive use and relatively high survival in Steamboat Slough (up to 41.5% routing through and up to 39.8% survival), part of the Sacramento River's distributary network. Migration through this pathway precludes juvenile salmon from encountering junctions leading to low survival routes. Results from this modeling effort provide valuable information and highlight opportunities for directing management actions to benefit these ecologically and economically valuable runs of Chinook Salmon.