Recent groundwater geochemical data from boreholes and surface recharge water in the Quaternary aquifer in the flood plain aquifer of the Beni Suef area have been utilized to try to assess the evolution of groundwater composition. The Nile flood sediment contains abundant sand and clay minerals. Evaporite minerals are common in the marl and marly carbonate deposits along the western and eastern flanks of the flood plain aquifer. The area characterized by high activities concerning agricultural, urbanization and reclamation and cultivation of the desert fringes along the western and eastern borders of the valley. The flood irrigation system and the lack of sewage network, in most of the area, deteriorate the groundwater aquifer. The least geochemically-evolved groundwater types groundwater type 1 (GWT1) and groundwater type 2 (GWT2) inevitably have salinity slightly higher than the surface waters (SW) which is the main recharge source of the aquifer. They have similar cation and anion ratios (approximately equal molar quantities of Cl, HCO3, SO4, Na, Ca and Mg) although they have a significantly lower pH than recharge waters due to a possible combination of soil gas CO2 dissolution and dissociation. Sulphate reduction and de-nitrification of the oxidized forms of nitrogen reduced the NO3 concentration of the groundwaters than the SW. The majority of the groundwater samples have higher salinity than recharge waters with salinity dominated by HCO3 and Ca with subordinate SO4 and Mg and they marginally saturated with calcite and dolomite. Careful analysis of the data reveals that water geochemical evolution is the result of congruent dolomite, gypsum dissolution and clay mineral-hosted cation exchange (increasing Na and Ca). A small region of the aquifer displays an extreme degree of aquifer-groundwater interaction. The groundwater here is saturated with respect to calcite and dolomite. Another region, beneath urban areas, has historically experienced pollution, evidenced by locally elevated nitrate concentrations, has commensurately higher SO4, Cl, Ca and Na concentrations and is supersaturated with carbonate minerals. The main geochemical processes in the aquifer are congruent dolomite dissolution, gaining Na due to cation exchange, evaporite mineral dissolution reduction of SO4 and NO2 confirm the confined condition of the aquifer in most of the area.