In the Sahel region in Africa, and in most arid regions, groundwater is the crucial source for water supply since surface water is scarce. This study aimed to understand a complex geochemical mechanism controlling the mineralization process in the Taoudeni Basin. A thousand randomly distributed groundwater samples acquired from different aquifers were used for this research. The results show that the majority of the samples observed are of the Ca2+-Mg2+-HCO3− and Na+-HCO3− types depending on the different aquifers. Mg2+ and Ca2+ may react with HCO3− precipitating as calcite and dolomite. The Na+-HCO3− groundwater type is mainly derived from the ion exchange process. This type indicates a paleo-marine depositional environment or that it passes through paleo-marine channels. Calcium of the standard Ca2+-HCO3− groundwater type exchanges with the sodium. Groundwater is characterized by the water-rock interactions that indicate the chemical alteration of the rock-forming minerals influencing its quality by a dissolution. The δ2H and δ18O stable isotopes designate the evaporation importance in the basin and recharge with recent rain. The bicarbonate-type presence in groundwater suggests that it is young and fresh water. Multivariate statistical methods, notably Principal Component Analysis and Hierarchical Cluster Analysis, confirm affinities among the aquifers and identify three main clusters grouped into two water types. Cluster 1 consists of Infra-Cambrian and Quaternary aquifers, whereas cluster2 includes the Precambrian basement and Permian-Triassic aquifers.