We evaluated effects of selective withdrawal system (SWS) for water quality improvement adapted for climate change in the Urayama Reservoir. We applied a 3-D coupled hydrodynamic and ecological model of ELCOM-CAEDYM with four SWS operation scenarios under future period (2062-2070). In the reservoir, the future period simulations showed that SWS operation using a surface intake could increase water temperature and deepen the thermocline compared with the present period. On the other hand, SWS operation of intaking at 10-12 m depth in the future period increased the thickness of turbid water intrusions by deeping the thermocline and decreased phytoplankton biomasses by higher surface water temperature than the present period. Moreover the increase of cold-water release and the decrease of warm-water release were expected by the surface intake operation in the future period.