This paper provides an assessment of existing airborne baseline geophysical data in relation to the hydrogeological characterization of protected groundwater-dependent terrestrial ecosystems (wetlands) in Anglesey, Wales. The attenuation of the radiometric data identifies the main areas of water saturation in the very near surface. The radiometric data have the potential to identify additional areas where similar degrees of saturation exist. The data may therefore be used to help define extensions to existing site boundaries and to provide information in the assessment of new wetland areas. The radiometric data also show regional-scale transition from the Carboniferous Limestone in the east, important for water supply to the wetlands, to older more impermeable strata to the west. The conductivity data appear capable of mapping the lateral extent of clay accumulations, concealed below peat cover which can act as a confining layer to the bedrock aquifer. At the regional scale the data reveal the extent of a former Holocene lake system and the hydrogeological control of a Carboniferous limestone–sandstone contact. The data therefore provide a non-invasive spatially continuous, characterization of the sites, improving the understanding of their dynamic water balances and, potentially, guiding further ground assessments and invasive investigations.