The development of a three-dimensional variable density model providing a rare example of physically based island simulation enables the analysis of both freshwater volume and fluxes of submarine groundwater discharge. Numerical groundwater modelling of different climatic and abstraction scenarios supports technical and management options for improved and sustainable freshwater supply in atoll environments. In Kiribati, Tuvalu and the Marshall Islands, the concept of sustainable groundwater management with a focus on managing freshwater resources to maintain water quality suitable for potable purposes was reinforced. Communities have been provided with options for self-determination of groundwater management based on a variable abstraction rate predicated by changes in salinity that can be maintained over defined periods in different climate and water security situations. The socio-economic costs of maintaining an acceptable salinity or ‘freshness’ of the supplied water are beneficial in comparison with the costs of providing an alternate water source, e.g. desalination of sea water.