As meteorology is the driving force for lake thermodynamics and mixing processes, the effects of climate change on the physical limnology and associated ecosystem are emerging issues. The potential impacts of climate change on the physical features of a reservoir include the heat budget and thermodynamic balance across the air-water interface, formation and stability of the thermal stratification, and the timing of turn over. In addition, the changed physical processes may result in alteration of materials and energy flow because the biogeochemical processes of a stratified waterbody is strongly associated with the thermal stability. In this study, a novel modeling framework that consists of an artificial neural network (ANN), a watershed model (SWAT), a reservoir operation model(HEC-ResSim) and a hydrodynamic and water quality model (CE-QUAL-W2) is developed for projecting the effects of climate change on the reservoir water temperature and thermal stability. The results showed that increasing air temperature will cause higher epilimnion temperatures, earlier and more persistent thermal stratification, and increased thermal stability in the future. The Schmidt stability index used to evaluate the stratification strength showed tendency to increase, implying that the climate change may have considerable impacts on the water quality and ecosystem through changing the vertical mixing characteristics of the reservoir.