Sustainable agricultural practices have been extensively used to reduce water pollution; however, the effectiveness of these practices may be significantly affected by climate change. In this study, we assess the effectiveness of sustainable agricultural practices in reducing sediment and nutrient export to rivers under future climate conditions, using the Soil & Water Assessment Tool in a Portuguese river basin exposed to high levels of agricultural pollution. In our study, filter strips demonstrated a significant mitigation effect on sediment and nutrient increases under simulated climate change conditions, with maximum sediment export depletion reaching 65% and the highest nutrient export depletion observed at 35%. The implementation of multiple sustainable practices resulted in the highest depletions, with a notable 71% depletion in sediment export and a 35% depletion in nutrient export. Additionally, our research underscores the crucial role of filter strips and multiple sustainable agricultural practices in mitigating the projected rise in nutrient concentrations during summer, given the effect of climate change on river discharge. Further studies exploring sustainable agricultural practices across different climates and watersheds can improve our understanding of their effectiveness for adaptation to climate change.