A multi-tracer approach has been implemented in the southwestern part of the Lake Chad Basin to depict the functioning of aquifers in terms of recharge, relationship with surface water bodies, flow paths and contamination. The results are of interest for sustainable water management in the region. The multi-layered structure of the regional aquifer was highlighted with shallower and intermediate to deep flow paths. The shallower aquifer is recharged with rainwater and interconnected with surface water. The groundwater chemistry indicates geogenic influences in addition to a strong anthropogenic fingerprint. The intermediate to deep aquifer shows a longer residence time of groundwater, less connection with the surface and no to only a little anthropogenic influence. Ambient Background Levels (ABLs) and Threshold Values (TVs) show the qualitative status of the groundwater bodies and provide helpful information for water resources protection and the implementation of new directives for efficient and more sustainable groundwater exploitation.