The hydrogeological system in the upper basin of Oum-Er-Rabiaa, characterized by a semi-arid climate, is facing ongoing water quality degradation primarily due to rising salinity. This study applies geochemical and stable isotope tracers to investigate the impact of geogenic features and processes on the origin and geochemical characteristics of water bodies. Hydrochemical analysis reveals significant spatial variation in mineralization, with two distinct groups of springs: (i) freshwater springs with high flow rates (approximate to 12-14 m3/s) and low salinity (approximate to 0.7 g/L) and (ii) saline springs with lower flow rates (approximate to 0.8-0.9 m3/s) and high salinity (approximate to 19 g/L). This variation reflects a transition in water chemistry from Calcium-Magnesium-Bicarbonate type in less saline waters to Chloride-Sodium-Potassium type in more mineralized waters. The main geochemical processes contributing to salinity include water-rock interaction, ion exchange, and residence time. Isotopic tracing identifies potential recharge areas originating from the high elevations of the Middle Atlas Mountains, through outcrops of Liassic limestones and Triassic sedimentary formations. It also highlights an evaporation process occurring within the system, which increases salinity in many locations.