Abstract Ecosystem-based management (EBM) is widely applied in marine and coastal ecosystems. However, its implementation in river basins is limited. This limitation is attributed to the lack of practical tools, which combine the general principles of EBM and the unique features of river ecosystems, to provide information for policy-making. A method to support EBM in rivers is proposed in the present study. This method analyzes the ecosystem by quantifying multiple relationships among natural and human components and considering the spatial heterogeneity in external activities and ecosystem resilience. Using this method, policies are prioritized in an EBM plan by systematically evaluating the effects of external activities on the ecosystem services. The application of this method in policy-making in the EBM context is presented in a case study using the Yellow River in China. As a practical tool, this method can help practitioners improve the implementation of EBM in river ecosystems.