This research investigates the effect of climate change on the thermal structure of lakes in response to watershed hydrology. We applied a hydrodynamic water quality model coupled to a hydrological model with a future climate scenario projected by a GCM A2 emission scenario to the Yongdam Reservoir, South Korea. In the climate change scenario, the temperature will increase by 2. 1°C and 4. 2°C and the precipitation will increase by 178. 4 mm and 464. 4 mm by the 2050 and 2090, respectively, based on 2010. The pattern changes of precipitation and temperature increase due to climate change modify the hydrology of the watershed. The hydrological model results indicate that they increase both surface runoff itself and temperature. The reservoir model simulation with the hydrological model results showed that increasing air temperature is related to higher surface water temperature. Surface water temperature is expected to increase by about 1. 2°C and 2. 2°C from the 2050 and 2090, respectively, based on the 2010 results. The simulation results of the effects of climate warming on the thermal structure of the Asian Monsoon Area Lake showed consistent results with those of previous studies in terms of greater temperature increases in the epilimnion than in the hypolimnion, increased thermal stratification, and decreasing thermocline depths during the summer and fall. From this study, it was concluded that the hydrodynamic water quality model coupled to the hydrological model could successfully simulate the variability of the epilimnetic temperature, changed depth and magnitude of the thermocline and the changed duration of summer stratification.