Vis Island is situated in southern Croatia. The island is mostly composed of karstified carbonate rocks and belongs to the Dinaric karst region, which is a locus typicus of karst landforms. Located far from the mainland, Vis island has maintained a successful water supply from its own karst aquifer for decades. Hydrogeological research has been undertaken to protect this excellent karst aquifer by establishing sanitary protection zones and to explore the possibility of increasing the pumping yield. New groundwater velocity data obtained via a tracer test were in accordance with the rock mass hydraulic conductivity calculated from previous pumping tests. The hydrochemical interpretation indicated several different phenomena, from carbonate and sulfate rock dissolution to seawater mixing with groundwater. A conceptual model of the island’s aquifer was improved, and two main catchments were delineated according to tracer test results, and connected with the geological setting, hydrochemical data, and new climatological insights. Such an approach is applicable for similar karst aquifers, in which topographic and hydrogeological divides usually do not coincide.