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The United Nations Water Conference 2023 highlighted the need for concrete actions to boost integrated water resources management for achieving the Sustainable Development Goals and called for strategies to enhance cooperation among stakeholders. Technical cooperation between countries and institutions in transboundary systems, e.g., on environmental data collection, is an effective way to promote international diplomacy and prevent disputes between riparian states. Still, establishing collaborations to inform bilateral dialogues on the identification of environmental challenges, their causes, and development priorities may be a difficult task in itself. This is particularly true in the African context because of limited resources and lack of data. In this paper, we analyse the case of nine transboundary river basins in Sub-Saharan Africa to identify which water-management challenges are perceived as most important by the different riparian countries from a policy and scientific perspective. Our insights are based on the most up-to-date scientific papers, open access reports and technical literature, river basin authority's strategy papers, projects' summary reports, and national policy documents. We also complement these sources with the pieces of information we gained through collaborations with regional and local experts, and management bodies (such as river basin authorities). We highlight the current water-related conflicts and the gap between the priorities identified by the scientific community and different riparian countries on how to tackle hydro-climatic change and improve food and energy security, human and environmental health. Based on our experience, we discuss some keys to building trust among stakeholders, strengthening cooperation, and identifying shared water-governance measures in transboundary river basins. They are: (i) connect science and policy to provide sound knowledge for the right questions, (ii) value local knowledge and exploit the complementarity of different perspectives, (iii) consider multiple spatial scales and multi-level stakeholders to leave no one behind, (iv) promote a culture which values trade-offs and handles complexity, and (v) co-create data and knowledge to facilitate stakeholder dialogue from problem definition to intervention identification. [Display omitted] • We implement activities in Sub-Saharan Africa for transboundary cooperation on water management. • We combine literature review, policy documents, and local experts' knowledge to identify water challenges. • Water priorities in policy documents and scientific literature sometimes do not match. • Lack of data, data sharing and consensus on data quality are common and undermine cooperation. • Science-policy-stakeholder collaboration can improve water management by compensating for data gap. [ABSTRACT FROM AUTHOR]