Abstract Water User Associations are community-based institutions that cover segments of rivers and are responsible for water management decisions. These are the result of institutional blueprints designed by the international community, widely adopted around the world. However, the implementation gaps between these generic institutional designs and the working on the ground are vast and require site-specific information to support water management decisions at the local scale. We used a hydrological modelling approach to assess how community-based decisions can maximize their outcomes and improve overall availability of water resources in the Great Ruaha River Catchment in Tanzania, a catchment that is under severe drought pressures and is of the utmost ecological, social, and political relevance at the national scale. We provide information to support decisions on when and where to focus conservation and management strategies by identifying the seasonal and spatial variability of water availability in the catchment. Our methods have the potential to be used in other catchments around the world. This study shows the importance of assessing the hydrological processes affecting the geographies of community-based institutions to identify priority areas of action.