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Neogene non-marine sedimentary rocks of the Bekaa Valley (Lebanon) are microfossil rich and show minimal lateral facies changes and post-depositional diagenetic alteration across continuous exposures. In this paper, we analyze the sedimentary facies and microfossils of three closely-spaced stratigraphic sections near the town of Zahle. The sedimentary sequence is divided, from base to top, into three intervals: (1) a massive conglomerate unit interpreted as alluvial fan deposits, (2) fossiliferous yellowish marls and limestone interpreted as perennial lacustrine deposits, and (3) an organic-rich marlstone intercalated with volcanic ash horizons interpreted as a palustrine interval representing an overall shallowing sequence. Intervals 2 and 3 contain a diverse microfossil assemblage comprising charophytes, terrestrial molluscs, a freshwater bivalve, ostracods as well as fish and mammal remains. The palaeoenvironmental characteristics and evolution of these lacustrine deposits are inferred through facies analysis and through comparison of microfossil tolerances with the ecological requirements of their nearest living relatives. Results suggest that during the Miocene the Bekaa Valley was occupied by a relatively shallow, stable, oligotrophic freshwater or slightly oligohaline lake that evolved to a very shallow eutrophic lake with a dense palustrine vegetation belt. The palaeolake ultimately regressed to the south due to climatic changes and tectonic stresses leaving the lacustrine deposits exposed in the area of Zahle as an erosional surface.