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The Agadir-Essaouira area in the occidental High Atlas Mountains of Morocco is characterized by a semi-arid climate. The scarcity and quality of water resources, exacerbated by long drought periods, constitute a major problem for a sustainable development of this region. Groundwater resources of carbonate units within Jurassic and Cretaceous aquifers are requested for drinking and irrigation purposes. In this study, we collected 84 samples from wells, boreholes, springs, and rivers. Hydrochemical and isotopic data were used to examine the mineralization and origin of water, which control groundwater quality. The chemical composition of water seems to be controlled by water-rock interactions, such as dissolution of carbonates (calcite and dolomite), weathering of gypsum, as well as ion exchange processes, which explain the observed variability. Stable isotopes results show that groundwater from the mainly marly Cretaceous aquifer are submitted to an evaporation effect, while samples from the chiefly calcareous Jurassic aquifer indicate a meteoric origin, due to a rapid infiltration of recharge runoff through the karstic outcrops. The low values of delta O-18 and delta H-2 suggest a local recharge from areas with elevations ranging from 400 to 1200 m for the Cretaceous aquifer and from 800 to 1500 m for the Jurassic units.