The intense use of water for both public supply and agricultural production causes societal conflicts and environmental problems in the Brazilian Federal District. A serious consequence of this is nonpoint source pollution which leads to increasing water treatment costs. Hence, this study investigates in how far agricultural Best Management Practices (BMPs) might contribute to sustainable water resources management and soil protection in the region. The Soil and Water Assessment Tool (SWAT) was used to study the impact of those practices on streamflow and sediment load in the intensively cropped catchment of the Pipiripau River. The model was calibrated and validated against measured streamflow and turbidity-derived sediment loads. By means of scenario simulations, it was found that structural BMPs such as parallel terraces and small sediment basins (‘Barraginhas’) can lead to sediment load reductions of up to 40%. The implementation of these measures did not adversely affect the water yield. In contrast, multi-diverse crop rotations including irrigated dry season crops were found to be disadvantageous in terms of water availability by significantly reducing streamflow during low flow periods. The study considers rainfall uncertainty by using a precipitation data ensemble, but nevertheless highlights the importance of well established monitoring systems due to related shortcomings in model calibration. Despite the existing uncertainties, the model results are useful for water resource managers to develop water and soil protection strategies for the Pipiripau River Basin and for watersheds with similar characteristics.