The propagation patterns of nitrogen during rainfall events are unsteady and heterogeneous due to the characteristics of generation and transport mechanisms. A simulation of non point source pollution was performed using GRASS-AGNPS to examine efficient management methods for diffusive pollution. Digital Elevation Model(DEM) was prepared to estimate the impact of topography on the transport pattern of diffusive pollutant Hanjaechon watershed on the Kyungbook province was selected as a study ares. Water quality samples were collected and analyzed for the calibration of the model. A heuristic approach was employed to improve the model performance. The model could successfully produce spatial distributions of nitrogen. The constructed map-layers may help to decision makers to determine the best management practices.