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Drinking water supply for the indigenous community on Milingimbi Island in the Northern Territory of Australia, is sourced from a freshwater lens beneath the island. Recent studies have suggested that this resource, vulnerable to saltwater intrusion, may not be capable of supplying the future water needs of the community because of the combined effects of climate change and projected demand. This study examined the value of complimentary hydrogeophysical data sets, specifically surface nuclear magnetic resonance (sNMR) and air and ground EM, to extend an understanding of the Islands’ groundwater system, and assist in the management of the aquifer systems present, including development of new production bores for supplementary water supply to the community. The geophysical data indicated that the freshwater resource on Milingimbi extends to ∼50m below the surface, largely confined to the weathered Cretaceous sedimentary package, but extending into underlying Cambrian metasediments. Geological logs indicate that the Islands’ aquifer system is spatially complex in composition. The sNMR data suggests that it is characterised by significant variations in lateral and vertical hydraulic properties. Modelled sNMR data and EM data imply that the sedimentary sequence should be considered as a fully connected, unconfined aquifer, with interconnected, higher yielding, facies.