Mara River basin is an internationally acclaimed and ecologically significant basin in the Lake Victoria basin. The recent trend in major land use change in the upstream (forest-to-agriculture conversion) has been the major driver for the current hydrologic alterations. Recent hydrologic data and observations show a reduction in dry season flow, increase in peak flows during wet seasons and an increase in sediment load. This has led to the need for more observation and modeling to understand the impacts of the various land use changes on the sediment and runoff characteristics of the watershed . Two physically based models (Erosion 3D and Water Erosion Prediction Project (WEPP)) were applied to predict the watershed scale sediment and runoff response. Watershed scale modeling results show that sediment yield and runoff vary by slope, land use and soil type. The spatial sediment budget also shows the variability in the erosion and deposition of sediment in the basin. Average simulated erosion in cultivated land was about 120 t/ha/yr and the lowest simulated erosion rate was on bush lands and grasslands, which may indicate change in land use has significant impact on soil erosion in the Mara River basin. It was shown that both WEPP and EROSION 3D models are useful tools for watershed scale application and estimation of runoff and sediment yield. ► We estimated sediment yield and runoff at watershed scale using two soil erosion models. ► We evaluated the two models using field runoff and sediment data. ► We found that sediment and runoff varies by land use, topography and soil type. ► The two models were comparable but WEPP model was better for sediment estimation. ► Agricultural areas contribute about 50% of the sediment budget in the watershed.