The study area is located in a hyper arid area in the Western Egyptian Desert which represents a massive agricultural project where irrigation water is extracted from the Nubian sandstone aquifer. This study focuses on the hydrogeochemical processes and its impact on the quality of the groundwater aquifer. Based on the geomorphology; the study area includes five geomorphological units, Wadi Kurkur bediplain, Aswan High Dam Lake, The Nile Valley, West Dungul plain and basement outcrops. According to the geology; the study area is distinguished by sedimentary cover ranging in age from Upper Jurassic to Quaternary. Regarding the hydrogeology of the study area; the Nubian sandstone aquifer is the main aquifer in the study area where it is represented by 24 groundwater samples plus one sample from the stem of the Lake Nasser. All samples were collected, analyzed and interpreted. Groundwater salinity classification shows that all the groundwater samples are fresh water type except one sample considered brackish water type. The pH values of the selected groundwater samples vary from 5.8 in the center to 7.6 in the Northern side with median value of 7.3. The groundwater's temperature ranges from 26.2 to 38.4 C. The relationship between salinity content and the other ions show a strong correlation between the values of Ca2+, Cl− and SO42− with the TDS values and a moderate correlation between Na+ values with TDS values. Silicate and carbonate weathering are the main hydrochemical processes affecting the groundwater. From the saturation indices (SI) results it is indicated that Gypsum, Anhydrite and Manganite dissolve with negative SI values, whereas iron minerals are supersaturated with positive values. From the hypothetical salts, it is indicated that the Nubian sandstone groundwater in the study area is highly evolved as it's enriched with terrestrial and marine residuals. From the Mixing Model, it is indicated that the Nubian sandstone aquifer has paleowater contribution percent ranging from 81 to 92% and Lake Nasser water contribution percent ranging from 7 to 18%. The Nitrate concentrations are below the maximum allowable limits of the WHO, however high concentrations of heavy metals were recorded in the groundwater samples at various extents.