Stable ( 2H and 18O)and radioactive isotopes ( 3H and 14C) allow the identification of the pattern of the regional groundwater flow in the Bilma-Djado basin. The general trends of groundwater flow are from the east (Tibesti) to the west (Djado basin), and, to a minor extent, north-south along the Bilma ridge. Another component has been noticed linked to wadis subsurface runoff flowing from Hoggar towards the south-east. The main recharge areas for the aquifers are the Tibesti massif (Holocene recharge) and the eastern border of the Hoggar (present day recharge). The presence of tritium indicates an upward leakage from the Cambro-Ordovician aquifer (2.5 ± 1.0 TU) to the Visean aquifer (1.8 ± 1.0 TU) and the Continental Intercalaire aquifer (2.9 ± 1.0 TU). The main discharges are the direct evaporation of the aquifers and some springs in the border of the Bilma-Djado basin supplied by the Cambrian aquifer. Only in this case, the waters are not affected by the isotopic fractionation effect and lie close to the classical meteoric water line for groundwater recharged during Holocene (5‰).