Best management practices (BMPs) are a way to control pollution in river basins. Prioritization of BMPs helps improve efficiency and effectiveness of pollution reduction, especially in critical source areas (CSAs) that produce the highest pollution loads. Recently, the Dez River, Khuzestan, Iran, has become highly eutrophic from overuse of fertilizers and pesticides. Dry and irrigated farming produce 77.34% and 6.3% of the total nitrogen (TN) load, and 83.56% and 4.3% of the total phosphorus (TP) load in this basin, respectively. Residential, pasture, and forest land uses account for 16.36% of the TN and 12.14% of the TP load cumulatively. In this study, the Soil and Water Assessment Tool (SWAT) was implemented to model the Dez River basin, and evaluate the applicability of several BMPs including point source elimination, filter strips, livestock grazing, and river channel management, in reducing the entry of pollution loads to the river. Sensitivity analysis and calibration/validation of the model was performed using the SUFI-2 algorithm in the SWAT Calibration Uncertainties Program (SWAT-CUP). CSAs were identified using individual (sediment, TN, TP) and combined indices, based on the amount of pollution produced. Among the BMPs implemented, filter strips were most effective in reducing TN loads (59%), and, increasing the D₅₀ of particles for river channel management was most effective in reducing TP loads (49%).