Developing environmental and chronological data for the Miocene and Pliocene successions of the central Sahara provide a basis for refining the pacing of green Sahara episodes to consolidate debate about early hominin dispersal from eastern Africa. Sedimentological, isotopic and geomagnetic polarity datasets are used to assess the environment and age of the Zarzur Formation in eastern Fezzan, Libya. A magnetostratigraphy based on four sections, combined with a statistical comparison to the geomagnetic polarity timescale, indicate that the formation was deposited from 7.8 Ma to 4.3 Ma. Lacustrine facies comprise laminated, peloidal mud-grade carbonates (with localised gypsum) formed in varying fresh to hypersaline inter-dune lakes. A second lacustrine facies comprises gastropod- and ostracod-bearing calcareous sandstones, formed in lakes developed on sandy substrates. These systems evolved from earlier fluvial and sandy-playa environments developed in the latest Tortonian. Based on δ13C and δ18O from carbonates formed in the lacustrine systems and calcrete-related cements, water sources for the lake deposits varied between low to high salinity and were largely from westerly moisture sources likely from extreme precipitation events. Groundwater was an important source for the inter-dune lakes because of irregularity in precipitation. The timing of lacustrine carbonate formation was in part paced to deep lakes that developed in the East African Rift in the early Pliocene, although sandy substrate lakes also formed during the Messinian. Greening of the Libyan Fezzan during deposition of the Zarzur Formation promoted potential habitat pathways for early hominid dispersal from the Megalake Chad Basin.