Groundwater of the Pliocene aquifer in Wadi El Natrun area represents the primary source of reliable water for drinking and agriculture uses. This research focuses on the study of the different sources of water in the study area and determines the origin and quality of this waterand also is interested in studying hydrogeochemical processes that affect them and the movement of water through the analysis and determine the activity of different elements, and also to changes in hypothetical salts with the direction of water flow in three sectors of the region and the statement of the most important geochemical processes that occur. Finally it is evaluated the suitability of the water for different purposes. The results show that, there is a zonation of chemical composition; this zonation is characterized by a change of cation species from dominantly Ca and Mg near the east to Na-dominated waters in the west. Mirroring this, anions change from HCO3 type to Cl and SO4 type.The ions displays two grades of metasomatism along flow path, first the stage of mineralization(HCO3>Cl>So4) at the east then the advanced stage of mineralization (Cl>SO4 >HCO3) at the west. According to the(W.H.O.2005), 45 % of tested groundwater samples are permissible for drinking. Most groundwater samples of the Pliocene according to SAR andRSC are suitable for irrigation purposes under normal condition, but all surface water samples (lakes) are saline water,so it is not valid for drinking or irrigation purposes.