There has been continuous efforts to manage the water resources for the required water quality criterion at river channel in Korea. However, we could not obtain the partial improvement only for the point source pollutant such as, wastewater from urban and industrial site through the water quality management. Therefore, it is strongly needed that the Best Management Practice(BMP) throughout the river basin for water quality management including non-point source pollutant loads. This problem should be resolved by recognizing the non-point source pollutant loads from upstream river basin to the outlet depends on the land use and soil type characteristic of the river basin using the computer simulation by distributed parameter model based on the detailed investigation and the application of Geographic Information System(GIS). Used in this study, Annualized Agricultural Non-Point Source Pollution (AnnAGNPS) model is a tool suitable for long term evaluation of the effects of BMPs and can be used for un gauged watershed simulation of runoff and sediment yield. Now applications of model are in progress. So we just describe the limited result. However If well have done modeling and have investigated of propriety of model, well achieve our final goal of this study