The basement aquifers in Burkina Faso are increasingly exposed to groundwater pollution, largely due to socio-economic activities and climatic fluctuations, particularly the reduction in rainfall. This pollution makes the management and understanding of these aquifers particularly complex. To elucidate the processes controlling this contamination, a methodological approach combining principal component analysis (PCA) and multivariate statistical techniques was adopted. The study analyzed sixteen physicochemical parameters from 58 water samples. The primary objective of this research is to assess groundwater quality and deepen the understanding of the key factors influencing the spatial variation of their chemical composition. The results obtained will contribute to better planning of preservation and sustainable management measures for water resources in Burkina Faso. The results show that three principal components explain 72% of the variance, identifying anthropogenic inputs, with two components affected by mineralization and one by pollution. The study reveals that the groundwater is aggressive and highly corrosive, with calcite saturation. Water-rock interactions appear to be the main mechanisms controlling the hydrochemistry of groundwater, with increasing concentrations of cations and anions as the water travels through percolation pathways. PCA also revealed that the residence time of the water and leaching due to human activities significantly influence water quality, primarily through mineralization processes. These results suggest that rock weathering, coupled with reduced rainfall, constitutes a major vulnerability for aquifer recharge.