The present study focuses on the hydrogeological system of the Batha basin (Chad). This area is symptomatic of the functioning of an endoreic basin in an arid to semi-arid climate, of its water storage capacity related with the climatic fluctuations, and of the problems associated with assessing resources in this Sahelian zone. This basin forms the eastern part of the Lake Chad basin, which extends over 2.38 Mkm2. It is a vast sedimentary basin, filled by detrital and fluvial-lacustrine deposits of Eocene (Continental Terminal) to Quaternary age, and bordered by Precambrian crystalline formations. The study aims to assess the aquifer potential of the groundwater system and its dynamics using a combined geology-hydrogeology-hydrochemistry approach. The lithology defined an heterogeneous and multi-layered system. The piezometric map reveals the dynamics of the general groundwater flow direction SE-NW, suggesting the interconnection of the different parts of the aquifer system. Based on the concentrations of major ions in solution, the hydrochemical results have identified four main types of facies: calcium bicarbonate (dominant), sodium bicarbonate, sulphate-sodium and mixed. The mineralization of these facies appears to be essentially controlled by water-rock interaction and to a lesser extent by base exchange and evaporation process. Calculations of saturation indices indicate that these waters are close to equilibrium with the calcite-Mg phases, gaylussite and gypsum. Nevertheless, given the low and medium ionic contents, it appears that the groundwater in the Batha basin is moderately evolved. On the other hand, stable isotope analyses (δ2H and δ18O) of groundwaters show the existence of three compositional groups corresponding to: (A) ancient water disconnected from current meteoric influences, (B) mixtures of current meteoric water and older water affected by evaporation during infiltration, (C) mixtures of current and ancient meteoric water more impacted by the evaporation process. In addition, tritium (3H) analysis of these waters shows the existence of three composition groups corresponding to current rainwater, modern water and post-modern water. Taken together, these results show that the hydrogeochemical differentiations obtained from both ionic and isotopic analyses cannot be strictly associated with the different aquifers (Quaternary, Pliocene, CT and basement). This confirms the interconnection of the Batha system and suggests that the heterogeneity observed is mostly controlled by lithological and climatic variations.