In tropical basaltic volcanic islands, aquifers’ hydraulic properties are largely controlled by the intensity of weathering of volcanic rocks, which in turns dictates groundwater gradients and the geometry and thickness of the freshwater lens. We explore the role of spatial variability in downward weathering affecting basaltic lavas and tuff cones of different ages on the extent and geometry of the freshwater lens in Wallis Island, Territory of the Wallis and Futuna Islands, South-West Pacific, which is relied upon for water supply, and which some wells are locally subject to saline intrusion. Geological, hydraulic and geophysical data were integrated in a 3D numerical variable-density groundwater model of the island. Data and model results showed that deeper weathering affects older lava flows non-uniformly depending on the island’s tectonic setting and suggested the existence locally of younger un-weathered lavas overlying deeply weathered lavas. Hydraulic conductivities range from 10-2 m/s in un-weathered lavas to 10-4 m/s in the most deeply weathered rocks. Higher groundwater salinities and lower water table were observed and modelled in wells located in young un-weathered lavas, or in old lavas with shallow weathering regardless their distance to the shoreline. Deeply weathered lavas are therefore less vulnerable to saltwater intrusion. Locally, the existence of low permeability tuff cones, more prone to weathering, also act as relative barrier to saline intrusion. Findings are consistent with the history of development and operation of the well fields located across these different units.