Coastal aquifers provide a source of water for more than one billion people, with island freshwater lenses being some of the most vulnerable coastal groundwater systems due to their susceptibility to saltwater intrusion. Basic hydrogeological and hydrochemical knowledge regarding the recharge and salinisation processes of freshwater lenses is important to ensure sustainable utilisation, especially considering possible climate change effects. This paper makes an assessment of the fate of a freshwater lens in a drying climate through a comparison of current and historic hydrochemical data, which to the author's knowledge is unique to this study. Fresh groundwater stable isotope signatures (δ18O, δ2H) reflect local amount weighted rainfall signatures (δ18O: −3.8‰; δ2H: −15.1‰), and confirm rainfall as the origin of fresh groundwater (δ18O: −4.47 to −3.82‰; δ2H: −20.0 to −16.6‰). Mixing with seawater was identified through enriched groundwater δ18O and δ2H signatures (maximum values of −0.36‰ and −1.4‰ respectively) compared to local rainfall and higher salinity (maximum 29,267 mg/L Total Dissolved Solids (TDS)) in a number of monitoring wells around the freshwater lens. Enhanced seawater intrusion detected in the northern section of the lens area was identified through significantly increased TDS values over the last 20–40 years, with increases of up to 3000% observed between 1990 and 2014. A reduction in the extent of freshwater by approximately 1 km2 was identified since 1977, which was found to be primarily caused by a reduction in recharge to the freshwater lens due to a ∼20% decline in winter rainfall in the south-west Western Australian region since the mid 1960s. Groundwater abstraction was found to equate to between 5% and 9% of the estimated recharge for the island, and is not a significant factor in the reduction of the lens extent compared to the observed decline in rainfall recharge. Interestingly, seawater intrusion into the fresh water lens was found to occur by older seawater (0.03–0.09 TU) in regions of the lens that were previously fresh or slightly brackish, while one sample (0.67 TU) suggests either modern seawater intrusion or mixing of older saline groundwaters (>60 years) with rainfall recharge. The use of tritium dating in this island aquifer was essential in identifying ‘older’ seawater that was previously unidentified until now. The isotopic and hydrochemical tools used in this paper quantify the effects of groundwater abstraction and climate variability on the freshwater lens and have implications for the sustainable management of the groundwater resource on Rottnest Island, and elsewhere.