According to previous studies, the increased air temperature can lead to change of thermal stratification structure of lakes and reservoirs. The changed thermal stratification may result in alteration of materials and energy flow. The objective of this study was to predict the effect of climate change on the water temperature and stratification structure of Daecheong Reservoir, located in Geum River basin of Korea, using a three-dimensional (3D) hydrodynamic model (ELCOM). A long-term (100 years) weather data set provided by the National Institute of Meteorological Research (NIMR) was used for forcing the 3D model. The model was applied to two different hydrological conditions, dry year (2001) and normal year (2004). It means that the effect of air temperature increase was only considered. Simulation results showed that the surface water temperature of the reservoir tend to increase in the future, and the establishment of thermal stratification can occur earlier and prolonged longer. As a result of heat flux analysis, the evaporative heat loss can increase in the future than now and before. However, the convective heat loss and net long wave radiation from water surface decreased due to increased air temperature.