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Small-scale fisheries in inland waters are particularly important for supporting local communities, providing livelihoods, and ensuring food security, especially in rural areas along or around existing water basins. However, these food systems are vulnerable to stressors such as pollution, habitat loss and degradation, draining wetlands, river fragmentation and poor land management. Indeed, there is potential to increase synergies between these different sectors using “integrated water resources management” (IWRM). There are currently no global or regional frameworks between regional fishery bodies (RFBs) and basin management organizations (BMOs) in place to exploit synergies between inland fisheries and other water use sectors. Consequently, the overall objective of the first global workshop between RFBs and BMOs, held in Entebbe, Uganda from 6 to 8 December 2023 was to promote, discuss and establish an effective cooperation framework between BMOs and RFBs and to develop concerted approaches to integrate inland fisheries management into basin management, in the context of climate change, water scarcity, food security and ecosystem health. The workshop report will share the outcomes from this workshop which resulted in a consensus on the importance of employing multidisciplinary approaches, recognizing their value and the imperative need for such strategies.