Changes in water temperatures caused by climate change in California's Sacramento–San Joaquin Delta will affect the ecosystem through physiological rates of fishes and invertebrates. This study presents statistical models that can be used to forecast water temperature within the Delta as a response to atmospheric conditions. The daily average model performed well (R2 values greater than 0.93 during verification periods) for all stations within the Delta and San Francisco Bay provided there was at least 1 year of calibration data. To provide long-term projections of Delta water temperature, we forced the model with downscaled data from climate scenarios. Based on these projections, the ecological implications for the delta smelt, a key species, were assessed based on temperature thresholds. The model forecasts increases in the number of days above temperatures causing high mortality (especially along the Sacramento River) and a shift in thermal conditions for spawning to earlier in the year.