In the Sohag Governorate, groundwater is a crucial source for rural households and public supply. Even some major villages rely on groundwater for drinking and irrigation. Groundwater in the investigated villages (i.e., Araya and Gaziert Shandwel) occurs in the Pleistocene porous aquifer resting on marine Pliocene clay sheets. The geochemistry and multivariate statistics (i.e., correlation matrix (CM) and cluster analysis (CA) have been utilized to assess processes affecting groundwater hydrogeochemistry and to investigate the degree of water-rock interaction and mixing processes. The major ions including (Ca2+, Mg2+, Na+, K+, SO42−, Cl−, HCO3−) and the minor (NO3−, NH4+, Fe, and Mn) chemical constituents were measured in all groundwater samples. The data show that the groundwater chemistry is mainly affected by the geologic setting and impacted by the intense use of chemical fertilizers and wastewater percolation. Groundwater classification, binary diagrams, and hydrochemical processes were anticipated to evaluate groundwater characteristics in the regions of interest. The major ions reveal two main water types: Na-HCO3 and Ca-HCO3. Based on the chemical analyses, groundwater hydrogeochemistry is distinguished into two categories. The correlation analysis results indicate that natural processes are the prevailing processes affecting the groundwater geochemistry, whereas cluster analysis indicates the possible effects of human activities on the groundwater chemistry of both villages.