The Water Erosion Prediction Project (WEPP) model was applied to seven paired, nested watersheds within the Mica Creek Experimental Watershed located in northern Idaho, USA. The goal was to evaluate the ability of WEPP to simulate the direct and cumulative effects of clear-cutting and partial-cutting (50% canopy removal) on water and sediment yield. WEPP was modified to better represent changes in the Leaf Area Index during post-harvest forest vegetative recovery. Good agreement between simulated and observed streamflow was achieved with minimal to no calibration over a 16-year (1992–2007) period. For the seven watersheds and the entire study period, the overall Nash-Sutcliffe Efficiency (NSE), Kling-Gupta efficiency (KGE), and deviation of runoff volume (DV) between observed and simulated daily streamflow ranged 0.58–0.71, 0.67–0.81, and −4% to 9%, respectively. Good agreement between predicted and observed suspended sediment yield was achieved through the calibration of a single channel critical shear stress parameter. For sediment yield, NSE, KGE, and DV ranged 0.62–0.97, 0.43–0.97, and −2% to 2%, respectively, for the calibration period, and 0.61–0.93, 0.42–0.95, and −24% to 13%, respectively, for the period of model performance assessment. Regression analysis of observed- and WEPP-simulated increase in water and sediment yield following clear-cut treatment was similar; however, the WEPP-simulated increase was lower compared to observations particularly from the partial-cut watershed. The variability in the critical shear parameter for different stream channels in the study watersheds was directly related to the observed mean particle size on the stream bed and suggests that applications of the WEPP model in ungauged basins could potentially set the critical shear parameter based on particle size. Overall, the simulated results demonstrate the potential of WEPP as a modeling tool for forestland watershed management, particularly for estimating the effects of forest harvest on hydrograph fluctuations and consequently, stream sediment transport.