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This study investigates the Batha endorheic basin in Chad, situated east of the Lake Chad basin in the arid to semi-arid Sahelian zone. This region has not yet undergone comprehensive geological and hydrogeological studies. More broadly, the transition zone between semi-arid and arid climates has been minimally explored. This research aims to evaluate the resources and dynamics of this multi-layered system using a combined geology-hydrogeology-hydrochemistry-isotopes approach. The multilayer system includes sedimentary layers (Quaternary, Pliocene, and Eocene) over a crystalline basement. A piezometric investigation of the system shows a general SE–NW groundwater, indicating an interconnection between all layers. Hydrochemical analyses identifies four main facies (calcium-bicarbonate, sodium-bicarbonate, sulphate-sodium, and mixed), primarily controlled by water–rock interaction with secondary influences from base-exchange and evaporation. Saturation indices indicate that these waters are close to equilibrium with the calcite-Mg phases, gaylussite and gypsum. Stable isotopes (oxygen-18 and deuterium) categorize groundwater into three groups: ancient water, recent and older meteoric water mixtures affected by evaporation, and mixtures more heavily impacted by evaporation. Tritium contents reveal three groups: current rainwater, modern water, and sub-modern water. These results indicate that ionic and isotopic differentiations cannot be strictly linked to specific layers, confirming the interconnected nature of the Batha system. The observed heterogeneity is mainly influenced by lithological and climatic variations. This study, though still limited, enhances significantly the understanding of the basin’s functioning and supports the rational exploitation of its vital resources for the Batha area’s development. Future investigations to complete the present study are highlighted. Full article