The Quaternary aquifer in the western Nile Delta is threatened by seawater intrusion. Few studies have integrated diverse techniques for the assessment of seawater intrusion in this aquifer. The present study aims to determine the geochemical processes and impact of seawater intrusion on this aquifer. To accomplish this investigation, the integration of hydrogeochemical, statistical, multivariate statistical, and graphical tools were implemented on 75 groundwater samples and 5 soil samples. The physicochemical variables were analyzed using hierarchical cluster analysis (HCA), saturation index (SI), ionic ratios, ionic relationships, the seawater intrusion index (SWI) and the correlations among 16 hydrochemical parameters, to identify the influencing processes of groundwater quality in the study area. According to the statistical study, the groundwater is divided into four groups. Those are distributed, from north to south: Group1 (G1), Group2 (G2), Group4 (G4), and Group3 (G3). The samples of G1 and G2 are distinguished by Na–Cl chemical type. While G4 has two main ion associations, HCO₃–Ca–Mg and Cl–SO₄–Na, G3 is characterized by HCO₃–Cl–SO₄–Ca–Na type. The processes that affect the chemistry of the groundwater are the seawater intrusion, ion exchange, silicate and Ca-rich mineral weathering, and mineral deposition. G1 and G2 groups are primarily influenced by seawater incursion, evaporation, and the ion exchange mechanism. In addition, the weathering of silicate minerals has a substantial effect on G3 and G4 groups, resulting in the creation of carbonate minerals.