This study is to assess the runoff characteristics of nonpoint source pollution loads for Jecheon and Jangpyeong stream watersheds located in the upstream of Chungju lake. The SWAT (Soil and Water Assessment Tool), a physically based distributed hydrological model was calibrated and verified using 5 years (2006 to 2010) streamflow and water quality data. The Nash-Sutcliffe model efficiency for streamflow was 0.60~0.92 and the determination coefficients for sediment, Total Nitrogen (T-N), and Total Phosphorous (T-P) were 0.53~0.71, 0.51~0.91 and 0.38~0.85 respectively. The results showed that the Sediment, T-N, and T-P of Jangpyeong stream were 40.0~60.9 %, 34.8~64.1 % and 76.5~83.9 % higher than Jecheon stream watershed during wet days. The results evaluated high NPS loads at Jangpyeong stream because the percentage of urban and upland crop cultivation area Jangpyeong stream watershed was higher than Jecheon stream watershed.