South European and Mediterranean countries traditionally suffer from water scarcity, especially the regions around the Mediterranean. In Cyclades, the effects of drought have historically been observed and tackled with small-scale applications, with the most efficient method being rainwater harvesting (RWH). RWH is an inherent aspect of the local population’s culture and architecture, since most houses have built-in water tanks and flat roofs to harvest as much rainwater as possible. In recent decades, the increase in local population and tourism have added additional stress to the limited water resources of the Cycladic islands. To overcome water shortages, most of the islands are equipped with desalination plants. Despite the use of these plants, RWH is still a vital source of water that is free and has zero carbon footprint. Thus, it is important to compare, assess and quantify the performance of this traditional water conserving method as a key water source for the islands’ water resources management, today and for the coming decades. In this research, we investigate and quantify the future performance of rainwater harvesting applications and their contribution to continuous, sustainable, and climate-resilient water supply. The results show a decrease in rainwater harvesting potential in most of the islands, as well as the negative effect of touristic activity on per capita water availability on the islands.