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The metamorphic basement units of the Upper Ouémé watershed in Benin have been investigated to identify the structural controls on aquifer properties, groundwater flow and water balance at large scale. Spatial analysis of borehole and hydrogeophysical data suggests that large-scale weathering profiles, aquifer transmissivity and storage properties are better correlated to a palaeo-weathering surface. Multi-model analysis, combined with assessment of nine transient numerical groundwater models against observations, suggests the best conceptualizations are those where hydraulic conductivity and specific yield are distributed within a weathered zone determined through interpolation of weathered zone thickness. When compared to previous studies, the general groundwater balance of simulated models suggests the groundwater system contributes, on average, 49.8 m3s−1to the river flow (mostly during the rainy season). The same volumetric flow would be lost to groundwater evapo-transpiration and deep/lateral drainage of the catchment. Borehole abstraction (about 7.5 m3s−1) represents only 6% of the average groundwater recharge and 1% of the average rainfall. This suggests that despite relatively low borehole productivity, the basement aquifer system still has an important unused potential for rural to mid-scale water supply and that, at present, the main external drivers for groundwater resource sustainability are changes in climate and land use.