Surface water quality has been identified as potentially vulnerable to climate change. This study assesses the impacts of climate change on the water quality of Hsinshan Reservoir, Taiwan, through CE-QUAL-W2 simulations. The model parameters were calibrated by field data collected during 2004–2008, and verified against observations made during 2009–2012. The projected temperature and precipitation data for the near- and long-term future were downscaled to regional and daily scales, and used to simulate the projected changes in water quality through the validated model. The simulation results were reported as probability-based cumulative distribution functions to access the impacts of climate change on water quality. The results indicated that the intensified thermal stratification caused by the rising temperature is the primary driver of water quality decline, which increases the probability of deep-layer oxygen depletion and the flux of limiting nutrients for algae growth, resulting in a higher risk of algal blooms and eutrophication. The adaptation strategies of multilevel-intake operations and increasing bottom-layer dissolved oxygen without destratification are recommended.