This study integrates multivariate statistical analysis and hydrogeochemical modeling to investigate the processes controlling the groundwater composition of a shallow aquifer where increased pumping rates and anthropogenic impacts were prevalent. Eighteen groundwater samples were collected and analyzed for major elements and selected heavy metals. The data were classified on the basis of multivariate statistical analysis into three clusters: C1 (Na-Cl facies), C2 (Ca-SO4facies), and C3 (Ca-HCO3facies). The application of factor analysis gave four factors affecting the groundwater chemistry, namely the salinization factor, anthropogenic/secondary enrichment factor, the secondary and the micro-nutrient fertilizers, and the aluminum fertilizer factor. The hydrogeochemical study of the groundwater revealed that the processes controlling the groundwater chemistry in the study area are mainly affected by the groundwater occurrence either to the east or to the west of Bahr Youssef Canal. Generally, the dominant hydrogeochemical processes affecting the groundwater are silicate weathering, ion exchange, irrigation return flow, gypsum applications in soil, and evaporation. The groundwater quality evaluation shows that water quality varies from fair to excellent for drinking purposes, where the best water is located in the northern and central parts of the study area. The suitability of groundwater for irrigation was evaluated using several indices indicating that groundwater is suitable for irrigation in the northwest and western parts of the study area. As some groundwater samples lie in high salinity classes on the US Salinity diagram, it is recommended to use this water for plants with good salt tolerance under good drainage conditions. The integration between the statistical and geochemical tools helps reveal the dominant processes through data reduction and classification.Supplementary InformationThe online version contains supplementary material available at 10.1007/s10661-023-11206-9.