To prolong the useful life of lakes and reservoirs, prioritizing watersheds by severity and risk of soil erosion is an essential index to develop sound sediment management plans. This study aims to predict soil erosion risk and sediment yield using Soil and Water Assessment Tool (SWAT) model in Lake Ziway basin, Ethiopia, and the model result is validated with lake bathymetric changes. The SUFI-2 program was applied for a model calibration and the performance of the model was assessed. The catchment prioritization study indicated that some sub-basins having the same soil type and land use but a higher slope gives higher sediment yield. This confirms that, in the basin, the upland is the main source of sediment for the lake, hence the variation of sediment yield is more sensitive to terrain slope. Furthermore, the soil conservation scenarios demonstrated in SWAT that reduce the slope length of the watershed by 50% for a slope greater than 5% are decreasing the sediment yield of the basin by 55%. The bathymetric differencing of the lake indicates that the sediment was accumulating at a rate of 3.13 t/ha/year while a calibrated SWAT model resulted in 5.85 t/ha/year. The identified reasons for these variations are the existence of outlet for the lake, floodplain depositions and abstraction of sediment (sand mining) from the tributary rivers before flowing to the lake.