The purpose of the present work is to identify the origin of replenishment and mineralization processes of lower Miocene Moghra aquifer at Wadi El-Farigh area and its vicinities. Hydrogeological, isotopic and hydrochemical studies were carried out. This aquifer is mainly composed of sand and sandstone with shale and clay inter-beds (fluviatile facies) at wadi El- Farigh area and changes to marine limestone and sandstone facies toward northwest. Its thickness shows gradual increase in the northwest direction, where, it ranges between 150 and 550 m and reaches more than 900 m at the west. Salinity content (TDS) of groundwater ranges from 222 to 667 ppm at W. El- Farigh area reflecting fresh water type. It increases to more than 3000 ppm at the west due to marine facies effect. The ionic concentrations of bicarbonates are the highest between the anions and followed by chloride and sulphate ions. Among the cationic concentrations the sodium ions prevail and followed by calcium and magnesium ions The dominant water type is Ca-Mg-Sodium, Cl-Bicarbonate, which indicates meteoric water genesis. The obtained results of the stable and radioactive isotopes contents revealed depleted oxygen18 and deuterium, absence of tritium and high carbon14 age. This indicates less active recharge and significant contribution for non regenerating paleowater that alarm a wise exploitation schemes for the groundwater resources. The paleowater component could be in part represented by intensive local paleometeoric water and in the other part paleo-Nile water entraped in the buried old Nile channels. The groundwater is suitable for domestic purposes and reflects a hazard for irrigation purposes due to sodium toxicity.