The purposes of this study were to identify the current potential sediment source areas and quantify rate of erosion and runoff. Runoff plots were established at three sites and the Water Erosion Prediction Project (WEPP) and Erosion 3D models were applied at watershed scale. The highest total sediment yield was observed on cultivated land (162.38 g/m2) in the Nyangores sub-watershed and the lowest sediment yield (29.95 g/m2) was observed on grassland, in Amala downstream. The model evaluation indicated that both of the models perform well in estimation of runoff, however, the WEPP model performs better than Erosion 3D in estimation of erosion. At watershed scale, the simulation result indicated that average erosion in cultivated land was about 120 tons/ha/year and the lowest erosion rate was estimated on bush lands and grass lands, which may indicate change in land use has significant impact on soil erosion in the Mara River basin