ABSTRACT The Soil and Water Assessment Tool Plus (SWAT+) model depends on the Modified Universal Soil Loss Equation (MUSLE), which in turn depends on the peak runoff rate for the estimation of soil loss from a catchment. The SWAT+ model generates a random number for each day in the process of peak runoff rate estimation from the catchment. On the other hand, the model provides calibration parameters like the peak rate adjustment factor for sediment routing in the tributary channels and main channels. There is uncertainty that how likely the SWAT+ model estimates the actual peak runoff rates. An improved MUSLE does not depend on the peak runoff rate, and, therefore, it minimizes uncertainty related to the peak runoff rate when estimating soil loss from the catchment in the SWAT+ environment. On the other hand, the effect of the topographic factor of the MUSLE or improved MUSLE on soil erosion and sediment transport is not explicitly explained. Therefore, we modify the source code of the SWAT+ model for sediment yield estimation by replacing the improved MUSLE and the best-fitted equations of the topographic factor in the source code. The modified SWAT+ model showed better performance than the original SWAT+ model.