Tracking terrestrial environmental change throughout the Neogene is a challenge, notably in areas such as Central Africa where the few available data consist of a few vertebrate fossil assemblages. Here we aim to quantify the evolution of the δ18O of the main water body between four Neogene wet episodes in the Chad basin, ranging from the Late Miocene to the early Pliocene. The δ18O of the open water body was inferred from oxygen isotope measurements of phosphate in the apatite of open water fish tooth enamel. The more open the fish habitat, the lower the δ18O, as revealed by the teeth of the large tiger fish (Hydrocynus) sampled in the four available Chadian vertebrate fossiliferous areas, i.e., Toros-Menalla (anthracotherid unit), Kossom Bougoudi, Kolle, and Koro Toro, all located in the Djurab Desert (Chad) and dated at 7.04 ± 0.18 Ma, 5.26 ± 0.23 Ma, 3.96 ± 0.48 Ma, and 3.58 ± 0.27 Ma, respectively. The δ18O values increased by ∼2‰ between the two sites having ages that bracket the Messinian time period, and there was a slight increase of ∼0.6‰ difference between the three Pliocene sites. These results reflect unambiguously change in the water cycle in Central Africa during the late Neogene, interpreted as a constant drying trend between the four successive wet episodes registered in the Djurab and a shift during the Messinian.