Study area: The coastal sedimentary basin including the Zou and Ouémé rivers in Benin. Study focus: River discharge loss is known to occur on the Zou and Ouémé rivers in southern Benin since a couple of decades ago. The reason behind this discharge reduction remained so far unclear. In this study, we focus on creating a 3D-numerical model of the system and on evaluating the sensitivity of leakage between the rivers and aquifers to various parameters. New hydrological insights for the region: Results show that leakages along the Zou river and Ouémé stream are tiny (i.e., ∼3% of the discharge losses). This implies that the observed water loss from the Zou and Ouémé rivers is not likely caused by the leakage (infiltration) along these rivers into the subsurface. The streambed conductance is found to be among the factors that impact less the computed leakages in the study area. This study has ranked the different hydraulic and storage properties in their order of importance with respect to the computation of river leakages along the concerned rivers. The determined rank of importance of the hydraulic and storage properties can guide river leakage modelling exercises in similar regions elsewhere.