The shallow groundwater of the multi-layered sedimentary basin aquifer of southwestern Nigeria was assessed based on its intrinsic vulnerability property. The vulnerability evaluation involves determining the protective cover and infiltration condition of the unsaturated zone in the basin. This was achieved using the PI (P stands for protective cover effectiveness of the overlying lithology and I indicates the degree of infiltration bypass) vulnerability method of the European vulnerability approach. The PI method specifically measures the protection cover and the degree to which the protective cover is bypassed. Intrinsic parameters assessed were the subsoil, lithology, topsoil, recharge and fracturing for the protective cover. The saturated hydraulic conductivity of topsoil, infiltration processes and the lateral surface and subsurface flow were evaluated for the infiltration bypassed. The results show moderate to very low vulnerability areas. Low vulnerability areas were characterised by lithology with massive sandstone and limestone, subsoils of sandy loam texture, high slopes and high depth to water table. The moderate vulnerability areas were characterised by high rainfall and high recharge, low water table, unconsolidated sandstones and alluvium lithology. The intrinsic vulnerability properties shown in vulnerability maps will be a useful tool in planning and monitoring land use activities that can be of impact in groundwater pollution.