The purpose of this study is the development of a system for estimating non-point sources pollutant loads from a watershed, which enables users to get insights of pollutant load distribution in the watershed during rain as well. Based on the Geographic Information System, this non-point source pollutant loading estimation system(NSPLES) consists of three distinct models such as a distributed rainfall-runoff model, a soil loss and delivery model, and a non-point source pollutant model. It also includes GIS modules for preprocessing the input data for the models and graphical postprocessing of the model outputs. The system output aren't only the hydrograph, sedimentograph, and pollutograph at the watershed outlet, but also various maps that show the distribution of soil loss over the watershed. The developed system was applied to the two upper stream areas of Sumjin river basin, Ssangchi and Gwanchon basins, and three rainfall events for respective subbasins during 1992 and 1998 were selected for the system application. The results of this showed relatively higher corelation between observed data and simulated data, and proved the applicability of the system.