The water-mineral interaction processes can strongly impact the quality of groundwater. The present study focuses on determining these processes and assessing their role on the groundwater evolution in Samalut aquifer which is composed of fractured and karst carbonates. The aquifer was recharged mainly from Nile floods before the construction of Aswan High Dam (AHD). Forty four groundwater samples of Samalut aquifer and three surface water samples of the Nile River, Ibrahimia Canal and Bahr Yusef Canal were collected and analyzed for major ions. The groundwater salinity ranges from 407 mg/l (well no. 33) to 2467 mg/l (well no. 17). It increases due northwest. Six representative rock samples of Samalut Formation were collected from its outcrops and drilled wells. The mineral composition of these samples has been identified by X-Ray Diffraction (XRD). They are composed of calcite, dolomite, gypsum, anhydrite, halite, illite and ankerite. The mineral-water interaction processes were determined by the inverse hydrogeochemical modeling using NETPATH. These processes include the precipitation of calcite, the removal of calcium and magnesium in exchange for sodium as a result of freshening by the recharge from the Nile, and the dissolution of gypsum.