GRASS-AGNPS model integrated with GIS was applied to rural watersheds having complex land use characteristics and evaluated for its applicability through calibration using observed data. The analyses of raster encoding accuracy and model behavior to runoff, sediment yields and nutrient loads for different cell-size showed that 150 m cell size indicated reasonable applicability of the model. Simulated runoff was in a good agreement with the observed data and simulated peak runoff rate was larger than the observed data. The sediment yield simulated by modified AGNPS model using irregular cell for forest area were less than that of the regular cell method. In predicting sediment yields, the result showed a different trend at each representative rural watershed. Nutrient loads simulated by the model were significantly different from the observed data.