The water pollution Accident in the South Han River is increasing due to increase of pollutants inflow from small streams from rural areas and reduced flow rate. This study predicted the change of water quality in the main stream of the South Han River due to climate change through the linkage of watershed and water quality models. Also, This study analyzed the effect of water quality improvement on Seomgang and the South Han River by securing the flow during the dry season. According to the scenarios for securing the river flow during drought season, the river flow in the Seomgang is increased up to 2.19 times, and the water quality during the drought season was improved up to 20.5%, TN 40.8%, TP 53.4%. Also, the water quality of the main stream of the South Han River improved to 5.22% of , 5.42% of TN and 7.69% of TP as the river flow was secured from the Seomgang. The result of this study confirms that securing the baseflow in the Seomgang according to the scenarios for securing the river flow during the dry season has a positive effect on the improvement of the water quality of the rivers in the main river of the Seomgang and South Han River. The results of this study will contribute to the establishment of reasonable management to improve the water quality of the main stream of the Seomgang and South Han River.