The production of Klamath River fall Chinook salmon is thought to be limited by poor survival during freshwater juvenile life stages, in part a result of Ceratonova shasta—a highly infectious disease that can lead to fish mortality. Higher flushing river flows are thought to affect the concentration of C. shasta spores, and in turn, juvenile salmon infection and mortality. The Stream Salmonid Simulator (S3) model was built to simulate the spatiotemporal dynamics of the growth, movement, and survival of juvenile salmon from spawning through migration in response to river flow, habitat availability, water temperature, and C. shasta spore concentrations. The S3 model has been calibrated to juvenile fall Chinook salmon abundances at a trap site within the Klamath River, and was designed to provide objective predictions of juvenile salmon abundance and survival in relation to proposed flow management alternatives and resulting fish infection and mortality by C. shasta.
