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Water temperature has manifold effects on the biology of Pacific salmon. Thermal optima enable Pacific salmon to maximize growth while temperatures above thermal optima can induce stress and lead to mortality. This study investigated the impacts of climatic changes and water management practices on Chinook and Steelhead smolts in the Columbia River Basin using an integrated earth system model and a multiple regression model that incorporated nonlinear survival responses to water temperature. Results revealed that the effects would vary significantly with the species, location, and climate change scenario. Mean survival rates may increase by more than 10% in Upper Columbia River, while reduce by 1 similar to 13% and 2 similar to 35% for Chinook and Steelhead smolts respectively, in the Lower Columbia River by 2080s. This study highlights the importance of integrating the nonlinear response of survival rate to river temperature and water management effects in climate change vulnerability analysis for salmonid stocks.