Perched groundwater resources on the northwestern coast of Egypt have thus far been little studied. However, if replenished by rainwater, they can provide a considerable amount of renewable water, i.e., for sustainable irrigation. These resources are limited, show different salinity contents and are endangered by overuse, pollution and by the sea level rising in the context of global warming. This paper presents new climatic data, geomorphologic, geologic, geochemical and hydrological researches in combination with remote sensing and GIS applications from Fuka Basin. Fuka constitutes a special synclinal basin where the interbedded limestone and clays have been folded into gentle synclinal structures. Fractured Middle Miocene limestone represents the bearing formation for the perched groundwater. According to the hydrogeochemical analysis and the PHREEQC model, the aquifer is recharged during the winter season by rainwater from the surrounding tableland and the chemical evolution of the perched water is attributed to water–rock interaction and mixing of fresh water with sea water. The salinity of the perched water ranges from 2,126 to 2,644 mg/L whereas for the deep groundwater it reaches 9,800 mg/L. The study explores origin and potential of the perched groundwater of Fuka Basin and gives recommendations for a future sustainable use and further investigations.