Paleocene–Eocene phosphorite beds from three major outcrops of the Maknassy-Mezzouna basin (Central-Tunisia) were geochemically investigated to improve local stratigraphy, determine their ages, and attempt to constrain ocean circulation. ⁸⁷Sr/⁸⁶Sr ratios of phosphate materials from the Chouabine Formation display a large variation even within the same deposit (⁸⁷Sr/⁸⁶Sr between 0.707782 and 0.707830). Based on the Sr isotope data obtained in teeth enamels, further supported by the results in coprolites, Sr isotope ages of 57 ± 1.1 Ma were attributed to Layers I and II, and 62 ± 1.4 Ma to Layer III. These results assign a Paleocene Epoch for the principal phosphate series. The ⁸⁷Sr/⁸⁶Sr value of teeth enamel sample from the upper phosphate bed suggests an age of 46 ± 1 Ma for this sequence. Furthermore, the Nd isotopic compositions of these samples were used as a tracer for seawater circulation. The ¹⁴³Nd/¹⁴⁴Nd values of the analyzed samples vary between 0.512174 and 0.512202, corresponding to εNd_CHUR between – 8.1 and – 8.4. These values are similar to those reported from Gafsa-Metlaoui basin, southern Tunisia and other North African phosphorite deposits. These data are reminiscent of those of the Atlantic Ocean, which is new argument of the overturning of Tethys Circumglobal Current during the Paleogene period. The obtained results suggest water exchange between Tethys and Atlantic Ocean during this period.