The scarcity of water resources with increasing demand made the evaluation of groundwater quality an urgent matter. Thus statistical analyses and hydrochemical models were conducted on 111 wells sampled from Pleistocene aquifer at Qena Governorate. Multivariate statistics revealed mixed processes affecting groundwater chemistry. Such processes expressed in terms of four rotated factors; these are mineralization (salinization), anthropogenic surface recharge, dissolution of ferromagnesian minerals, and oxidation factor. Aquifer salinization is evidenced by a lateral change in the basic hydrochemical characteristics from low mineralized Ca–HCO3, Mg–HCO3, and Na–HCO3 water types to highly mineralized Ca–Cl, Mg–Cl, and Na–Cl facies. Chloride-water species are associated with high-impact areas of chloride-rich sediments (dissolution of overlain saline sediments and marine Pliocene clay underneath). Piper diagram indicates desert wells are dominantly affected by saltwater intrusion from deep aquifers along fault planes under over-pumping. On other hand, shallow wells are the most affected by surface activities. Likewise, wells located in the vicinity of the industrial zone and sites of wastewater disposal. This raises questions about desert reclamation strategy and its impact on groundwater quality; hence this approach can be used as a basic tool for reviewing desert reclamation management strategies. CapsuleQuaternary freshwater aquifer in Egypt was exposed to salinization under desert reclamation, via dissolution of marine deposits and intrusion from deeper aquifers.