This paper analyzes the impact of two climate change scenarios on flow rate and water quality of the Yongdam Dam and its basin using CE-QUAL-W2 and SWAT, respectively. Under RCP 4.5 and RCP 8.5 scenarios by IPCC, simulations were performed for 2016~2095, and the results were rearranged into three separate periods; 2016~2035, 2036~2065 and 2066~2095. Also, the result of each year was divided as dry season (May~Oct) and wet season (Nov~Apr) to account for rainfall effect. For total simulation period, arithmetic average of flow rate and TSS (Total Suspended Solid) and TP (Total Phosphorus) were greater for RCP 4.5 than those of RCP 8.5, whereas TN (Total Nitrogen) showed contrary results. However, when averaged within three periods and rainfall conditions the tendencies were different from each other. As the scenarios went on, the number of rainfall days has decreased and the rainfall intensities have increased. These resulted in waste load discharge from the basin being decreased during the dry period and it being increased in the wet period. The results of SWAT model were used as boundary conditions of CE-QUAL-W2 model to predict water level and water quality changes in the Yongdam Dam. TSS and TP tend to increase during summer periods when rainfalls are higher, while TN shows the opposite pattern due to its weak absorption to particulate materials. Therefore, the climate change impact must be carefully analyzed when temporal and spatial conditions of study area are considered, and water quantity and water quality management alternatives must be case specific.