Water pollution presents a substantial environmental challenge with extensive implications for water resources, ecosystem sustainability, and human health. Using a South African catchment, this study aimed to provide watershed managers with a framework for selecting best management practices (BMPs) to reduce pollution and the related risk to river users, while also including the perspectives of key catchment stakeholders. The framework encompassed the identification of and consultation with key stakeholders within the catchment. A Multi-Criteria Decision Analysis (MCDA) methodology using the Simple Multi-Attribute Rating Technique for Enhanced Stakeholder Take-up (SMARTEST) was used to identify and prioritise suitable BMPs in a case study. Decision alternatives and assessment criteria as well as their weights were derived based on stakeholder responses to a two-stage survey. Stakeholders included those utilising the river for domestic and recreational purposes, municipal representatives, scientists, NGOs, and engineers. The assessment of decision alternatives considered environmental, economic, and social criteria. The aggregated scores for decision alternatives highlighted the significance of involving stakeholders throughout the decision process. This study recommends the pairing of structural and non-structural BMPs. The findings provide valuable insights for catchment managers, policymakers, and environmental stakeholders seeking inclusive and effective pollution mitigation strategies in a catchment.