n southern Benin, where population is growing and water demand for domestic activities is increasing, water balance assessment constitutes a serious concern about sustainability of water resources. Major ions have been employed with statistical methods to identify geochemical processes controlling groundwater quality. Multivariate statistical analysis (principal component analysis “PCA” and hierarchical cluster analysis “HCA”) revealed the main sources of groundwater mineralization. According to the hydrochemical data and the methods of treatment, groundwater mineralization in the investigated aquifer is caused by four main processes: 1) mixing with Nokoué lake and Porto-Novo lagoon salt water causing salinity to increase in the southern part of the aquifer; 2) anthropogenic activities; 3) cation exchange process; and 4) soil CO2 diffusion providing a large proportion of bicarbonates.