Environmental and behavioral controls on juvenile Chinook salmon migration pathways in the Columbia River estuary

Juvenile Chinook salmon population dynamics in the Columbia River estuary are influenced by physical processes, hatchery practices, and behavioral decision-making. To better understand how environmental forcing and swimming behavior influence estuarine migration and travel times, we developed an individual-based model (IBM) that uses 3-D outputs from a hydrodynamic model to simulate Lagrangian transport as well as swimming and bioenergetics sub-models to simulate active swimming and growth. Simulations were run in 2010 during the migration seasons for yearling and subyearling Chinook salmon. For both life history types, alternative behaviors were simulated, from random walks to behaviors that optimized efficient system migration for yearling Chinook salmon and growth for subyearling Chinook salmon. Simulation results compared well against observed data on travel times and common migration pathways; the simulated travel times for both yearling and subyearling Chinook salmon were within several hours of the observed travel times. In general, residence times and pathways were largely driven by river discharge and the phase of the tide. During periods of greater river discharge, simulated estuarine residence times were reduced and variability across individuals was minimal. The timing of estuarine exit was closely tied to the phase of the tide, with most simulated individuals exiting the system during the ebb phase. While travel times were largely driven by flow velocities, swimming behavior was likewise important. Simulated yearling Chinook salmon behaviors that optimized movement with surrounding flows resulted in reduced estuarine residence times when compared to passive and random walk behaviors. Similarly, simulated subyearling Chinook salmon behaviors that optimized growth directed individuals to shallow peripheral habitats, resulting in longer residence times and higher growth rates. Even if potentially important factors such as predator avoidance were not included, this IBM provides an informative tool to model migration pathways, growth, and residence times of juvenile salmon in an estuarine environment and could be used to inform management decisions by evaluating various scenarios.