A complete understanding of groundwater dynamics and its interaction with surface water under the impact of agricultural activities is vital for local agriculture, ecology, and residents of dry regions, which is not commonly recognized in arid areas. This research outlines the geochemical characteristics, recharge sources, and potential factors impacting groundwater quality in a new land reclamation located in the small basin of Abu Mina, which is part of the Western Nile Delta region.1 Thirty-one groundwater samples and two surface water samples were collected in 2021 to represent the Pleistocene aquifer and were subjected to multivariate statistical, hydrochemical, and stable isotope analyses. Data analysis demonstrates that Na+ > Ca2+ > Mg2+ > K+ and SO42– > Cl– > HCO3– > NO3– are the predominant cations and anions, respectively. Groundwater salinity ranged from 465.60 to 6455.18 mg/l, with slightly alkaline. Most of the water samples fall into one of three types of facies: Ca–Cl, Na–Cl, and Mixed Ca–Mg–Cl, in decreasing order. The meteoric genesis index (r2) indicates that deep meteoric water percolation dominates the Pleistocene aquifer. The aquiline diagrams, correlation matrix, and different ionic ratios indicate that evaporation, reverse ion exchange reactions, and the dissolution of carbonate and silicate minerals are the main processes governing groundwater chemistry. Factor analysis (FA) indicated that three factors explain groundwater hydrochemistry, accounting for 71.98% of the total variance. According to the rotating components matrix (F1–F3), the chemistry of the Quaternary aquifer is principally affected by evaporation, ion exchange reactions, and anthropogenic influences. Additionally, salinity increases due to the return flow of irrigation activities and mixing between old and recent water. The stable isotopes (δ18O and δ2H) indicate that the Quaternary aquifer receives groundwater recharge through the return flow of excess irrigation and canal seepage. Under desert reclamation conditions, groundwater salinization processes should be given special consideration. All groundwater samples are appropriate for agricultural irrigation based on the Sodium Adsorption Ratio (SAR), Permeability Index (PI), Percent Sodium (%Na), and Residual Sodium Carbonate (RSC).