Participatory approaches to water management, and specifically to transboundary river management, have been widely applied over recent decades. Regarding transboundary rivers, the active involvement of key actors in policy planning is of great importance. In this context, a participatory approach has been used to identify sectors of interest and priorities related to water and development in the Mékrou transboundary River Basin involving three countries: Benin, Burkina Faso and Niger. We conducted a web-based survey to quantify expert opinion on sectors of water management policy and priorities for the Mékrou River Basin. The same set of questions was then put to a sample of local stakeholders living in this river basin. Our analysis reveals some points of convergence and some discrepancies between the opinions of experts and local stakeholders. Overall, it provides a comparative analysis of how experts and local stakeholders prioritize water policy measures, which could influence decision-making.