We quantified effects of future climate warming on temperature and stability in a variably stratified, hypereutrophic reservoir with large fluctuations in water level by calibrating a 2-D model (CE-QUAL-W2, version 3.7.1, Portland State University, Portland, USA) of reservoir hydrodynamics using a time series (1992 to 2011) of inflow and air and water temperature. The model was then forced with increased air temperature projected by an ensemble of climate models that accounted for complex local topography and seasonality, with greater warming in summer. Warming increased annual evaporation rates by 2.6 to 7.9%. Water temperature increased by 0.44 (whole-reservoir; p < 0.05), 0.47 (epilimnion; p < 0.01), and 0.30 °C (hypolimnion; p < 0.05) per 1 °C increase in air temperature. Thickness of the epilimnion and hypolimnion diminished, with expansion of the metalimnion. Schmidt stability correlated with mean water depth over a wide range of depths (3.9 to 8.1 m; Adj. R² = 0.91 to 0.93; p < 0.001). Increased air temperature increased mean annual stability by 6.1 to 23.6 J m⁻² when depth was large and the reservoir stratified, but when depth was low (due to combined low inflow and, in preceding years, high withdrawals), inhibiting stratification, then water temperatures increased evenly (and more) throughout the vertical profile so change in mean annual stability was near zero (−0.1 to 1.1 J m⁻²). Combined effects of reservoir management (volume, timing, and elevation of water withdrawal) and climate warming (temperature of air and benthic sediment) can impact the hydrodynamic regime differently under variably stratified conditions with implications for release of phosphorus from sediment and vertical transport of phosphorus to the euphotic zone.