Fresh groundwater lens dynamics and transition zone geometries on small tropical islands have been investigated in a wide range of geological environments. However, the understanding of multi-aquifer fractured bedrock systems and how they respond to episodic wet season rainfall recharge is still limited. This study used a comprehensive suite of isotopic tracers, hydrogeological and near-surface geophysical methods to characterise the multi-layer aquifer system on Milingimbi, a small bedrock island located in the tropics of the Arafura Sea, Northern Australia. Near-surface geophysics was used to determine the subsurface structure of the aquifer, including the spatial extent and thickness of the fresh groundwater lens and the shape of the transition zone. Pore water chloride profiles, hydrochemistry, and δ18O and δ2H data supported the geophysics results. The lens was found to be 40 m thick on average, with an up to 70 m thick transition zone underneath. Water level time series data over 4 years showed that there was a strong tidal signal observed in the groundwater wells screened in the deeper aquifer and that the aquifer system showed a dynamic response to the wet season rainfall. Time series chloride and δ18O and δ2H rainfall and production bore data suggest that there was a freshening (i.e. lower salinity input) of the lens as a result of recharge during the wet season, which occurs up to 6 months after the event. Groundwater residence time indicators showed that the mean residence time in the lens was at least 25 years and the rate of recharge to the system was up to 200 mm y−1. The comprehensive data set, which is rather unique in its wide range of methods that were applied, resulted in a hydrogeological conceptual model of the multi-layer bedrock aquifer system of the island that also provides insight into the fresh groundwater lens and the transition zone geometry of similar island aquifer systems.