Generation and transportation of runoff and pollutant loads within watershed generated eutrophication at Daecheong reservoir. To improve water quality at Daecheong reservoir, the best management practices should be developed and applied at upper watersheds for water quality improvement at downstream areas. In this study, two small watersheds of upper Daecheong reservoir were selected. The Long-Term Hydrologic Impact Assessment (L-THIA) model has been widely used for the estimation of the direct runoff worldwide. To apply the L-THIA ArcView GIS model was evaluated for direct runoff and water quality estimation at small watershed. And the Web-based Hydrograph Analysis Tool (WHAT) was used for direct runoff separating from total flow. As a result, the $R^2$ (Coefficient of determination) value and Nash-Sutcliffe coefficient value for direct runoff comparison at An-nae watershed were 0.81 and 0.71, respectively. And the $R^2$ value and Nash-Sutcliffe coefficient value at Wol-oe were 0.95 and 0.93. The $R^2$ value of BOD, TOC, T-N and T-P at An-nae watershed were BOD 0.94, TOC 0.81, T-N 0.94 and T-P 0.89. And the $R^2$ value of BOD, TOC, T-N and T-P at Wol-oe watershed were BOD 0.80, TOC 0.93, T-N 0.86 and T-P 0.65. The result that estimated pollutant loadings using the L-THIA ArcView GIS model reflected well the measured pollutant loadings except for T-P in Wol-oe watershed. With L-THIA ArcView GIS model, the direct runoff and non-point pollutant (NPS) loadings in the watershed could be analyzed through simple input data such as daily rainfall, land uses, and hydrologic soil group.