Deep groundwater resources around the world represent an important potential unconventional source of water. Here we document an extensive (17.3 km3) fresh/brackish groundwater body preserved in a deep (between 800 and 2100 m) carbonate platform aquifer in southern Sicily (Italy), by using deep well data and a 3D hydrogeological modelling. We attribute the distribution of this fossil groundwater to topographically-driven meteoric recharge driven by the Messinian sea-level drawdown, which we estimate to have reached 2400 m below present sea level in the eastern Mediterranean Basin. The discovery of such an extensive and deep freshened groundwater has significant implications in terms of resource potential for southern Sicily and other Mediterranean coastal regions, that share similar geological setting and water scarcity issues.