Groundwater is often the primary source of freshwater supply on remote small islands, where it exists as a freshwater lens, it is extremely vulnerable to over-extraction, pollution and seawater intrusion. Ensuring long-term sustainable management of the groundwater resource is of the utmost importance when there are growing water demands, sea-level rise and/or recharge decline. This study used a three-dimensional (3D), variable-density numerical groundwater flow and solute transport model to investigate freshwater lens dynamics in a multi-layered aquifer system on a small tropical island. The model was used to explore the feasibility and impacts of increased groundwater demand on the freshwater lens, its volume, geometry as well as the thickness of the freshwater/saltwater transition zone. The risks of saltwater intrusion, both laterally from the ocean and by localised up-coning from the deeper, more saline aquifers beneath the freshwater lens, were also evaluated. Model calibration used observed hydraulic heads and salinity observations from pumping and observation wells. Subsurface bulk conductivity values, which were calculated from inverted airborne electromagnetic (AEM) data, and near-surface geophysical data, were used in the calibration process. The results showed that the hydraulic heads and observed salinity achieved the ‘best fit’ in the calibration process, whilst the addition of the geophysical data helped constrain lens geometry in the steady-state model. The models’ sensitivity to the range of measured salinities could be enhanced by improving the conversion factor between the derived AEM conductivity values and the observed salinity data. This would best be achieved by targeted monitoring wells and improvements in the sampling/restoration of existing ones. The numerical model was used as a framework to evaluate the key underlying hydrogeological processes on the island, as well as an important decision-making tool to ensure a sustainable and reliable water supply for the island community.