Saltwater intrusion is the greatest risk to coastal community water supplies where they are dependent on fresh groundwater as the main source of supply. For small, fractured bedrock island aquifers, the fresh groundwater lens dynamics and transition zone geometry are complex. This study investigated the impacts of projected increases in groundwater pumping on a fresh groundwater lens to evaluate changes to the lens geometry and localized up-coning from the deeper, more saline aquifers beneath a small bedrock island in the tropics. A combination of traditional hydrogeological datasets and an airborne electromagnetic survey were used to develop a three-dimensional density-dependent groundwater flow and solute transport model using the SEAWAT code. This investigation represents one of very few studies that have taken such an approach. The model was calibrated using observed groundwater hydraulic heads and chloride concentration data, and calculated chloride values based on bulk conductivity measurements determined from inverted geophysical data. A staged calibration approach was adopted, firstly assessing the time-average lens extent and geometry, and secondly considering the seasonal groundwater level response. In the calibration, the geophysical data helped constrain the lens geometry in the absence of hydraulic head and chloride data. The calibrated model was used to test scenarios where groundwater pumping rates were increased above the current demand of 452 m3 d−1, showing that the lens is likely to be stable, i.e., its available storage is not expected to contract excessively, for extraction rates of up to 3,000 m3 d−1. The combined use of geophysical data and a numerical modeling approach was advantageous in investigating the lens characteristics. It also demonstrated how these techniques can be used together to evaluate coastal water resources and to manage water supply risks for coastal communities. The study demonstrated that the freshwater lens can likely support the freshwater demands of the remote community, and is a preferred option compared with high-cost and more complicated options such as seawater desalination and managed aquifer recharge.