The small islands in the Mediterranean Sea suffer water shortages, aggravated by pressure from tourism during the dry season. Many are affected by the intense and increasing human water demand and the harsh climatic and geographic nature of the island terrain. The present study, carried out on the island of Favignana, Egadi Archipelago (southern Italy), evaluates the regime of recharge to the subsurface, and hypothesizes a solution for identifying the areas where groundwater is most abundant, as well as the best management options for human use. By means of hydrological measurements and chemical analyses, a specific location has been identified in the eastern sector of the island where groundwater has optimal quality and the water table is at a depth of only a few metres. In other areas of the island the groundwater is more saline, due to seawater intrusion, and it is present only at greater depths. The residents of the island have in the past lived harmoniously with the climatic and hydrological regime of the island, and have shown good ability to manage the groundwater resources, fed by the limited precipitation that comes in winter, using it as a supplement to the drinking water supply that comes from Trapani (mainland Sicily) by a submarine pipeline and by tanker. Optimized management of the groundwater resources could reduce the volume of freshwater transferred from the mainland.