San Francisco Estuary and Watershed Science

San Joaquin River-origin Central Valley Chinook Salmon are a species of conservation concern because they play an essential role in the health and function of California’s aquatic ecosystems yet experience low survival as juveniles pass through the Sacramento–San Joaquin Delta (Delta) on their way to the Pacific Ocean. We analyzed 8 years of juvenile Chinook Salmon acoustic telemetry data near the State Water Project and Central Valley Project in the South Delta to inform how hydrodynamic and environmental conditions affect fish movement. The behavior of Chinook Salmon in this area was related to simulated outputs from a high-resolution hydrodynamic model that used a continuous-time multi-state Markov model. A total of 839 fish were detected near the facilities, and the median time fish spent in the area was 33 hours. Flow conditions near the water projects strongly influenced juvenile Chinook Salmon movement patterns. For fish detected at the Central Valley Project trash racks and outside the radial gates to Clifton Court Forebay at the State Water Project, the strongest effects on movement were from upstream-directed net flow, time of day, and turbidity. Export operations drew fish movement into the water export facilities when exports were high and at night. Movements in West Canal between Highway 4 and the radial gates were influenced by tidal flow and net flow. Fish primarily moved downstream on the ebb tide, especially when exports were lower. Study fish near the water projects experienced high predation, which reduced sample size and increased uncertainty. Our study identified factors that drive juvenile Chinook Salmon movements near the water projects and can be used to inform water operations and management decision-making that may improve salmon survival in the Delta.