Sensitivity analysis on lake temperature under the A1B SRES climate change scenario has been evaluated by coupling MRI-GCM with 20 km outputs and the Biwa-3D integrated assessment model. The non-hydrostatic 3D hydrodynamic model featuring Very Large Eddy Simulation (VLES) has been verified and compared with field observations in 2002 (the present-day year, PDY). A significant temperature increase in surface water, recording more than 34 degrees in the East Coast of the North Basin of the Lake Biwa, has been projected for the simulation for the very hot year (VHY), determined from comparison with MRI-GCM output for the year 2099, which may induce a catastrophic impact on lake water quality during the period. Weak stratification is predicted to start from March in VHY, compared with observations of stratification that doesn’t commence until after April in PDY. The thickness of the epilimnion which is around 15–20 m in PDY increases to 25–30 m in August in VHY due to a much higher atmospheric temperature. According to the model outputs, the vertical mixing may not always decrease due to the accumulated heat in the hypolimnion which has a higher temperature than the temperature during the winter. Accumulated heat in the hypolimnion may induce catastrophic degradation in the lake ecosystem.