Water pollution is an increasing global concern affecting millions of people around the world, especially in arid to semi-arid areas. Management of water resources has become a crucial requirement for present times and specifically for future decades due to its detrimental impact on populations. The eastern High Atlas represents a demonstrative situation to highlight the problems in water-stressed areas. The eastern High Atlas of Morocco has a semi-arid climate and low rainfall (<200 mm), irregular in time and space. The hydrology of the studied basin is characterized by intermittent flows and frequent, sometimes intense, limited floods. The main aquifer corresponds to the Plio-Quaternary deposits containing an unconfined groundwater of low thickness, from 3 to more than 30 m. This aquifer is controlled by the Paleozoic basement-Mesozoic to Quaternary cover interface. The hydrogeological system is located in a structurally complex area. The fractured and weathered surface part of the basement, directly in contact with the cover deposits, is also permeable. This system is mainly recharged by the depletion of the seasonal groundwater which take place in the Mesozoic landforms during rainy periods. In this semi-arid area, we show that the water resources and their qualities are highly dependant on the climatic conditions and water-rock interaction. The H-2 and O-18 isotopes indicate that the recharge of the Plio-Quaternary aquifer is mainly through precipitation on the summits of the NW part of the basin. The H-3 isotope reveals that the waters in the basin are less than 50 years old, implying a rapid turnover. The reduced potential of the groundwater and its quality of medium to high alkalinity, limit its use for drinking and irrigation.