Abstract. The identification of priority management areas (PMAs) is essential for the control of non-point-source (NPS) pollution, especially for a large-scale watershed. However, previous studies have typically focused on small-scale catchments adjacent to specific assessment points; thus, the interactions between multiple river points remain poorly understood. In this study, a multiple-assessment-point PMA (MAP-PMA) framework was proposed by integrating the upstream sources and the downstream transport aspects of NPS pollution. Daning River watershed was taken as a case study in this paper, which has demonstrated that the integration of the upstream input changes was vital for the final PMAs map, especially for downstream areas. Contrary to conventional wisdom, this research recommended that the NPS pollutants could be best controlled among the upstream high-level PMAs when protecting the water quality of the entire watershed. The MAP-PMA framework provided a more cost-effective tool for the establishment of conservation practices, especially for a large-scale watershed.