The late Miocene Messinian salinity crisis (MSC) was a significant oceanographic event that caused widespread evaporitic accumulation throughout the Mediterranean Basin. Although multiple hypotheses exist regarding the origin of evaporitic and post-evaporitic deposits, researchers remain divided on the magnitude of base-level fall, and on whether these accumulations record deep-water or non-marine conditions. Here, we introduce a previously unknown, upper Messinian fluvial deposit comparable in size to the late Miocene Nile River fluvial valley fill and show that near-complete desiccation of the eastern Mediterranean was responsible for its development. The basin-wide accumulation, which is located offshore Cyprus, Syria, Lebanon, and Israel, lies directly atop deep-basin evaporites and related erosional surfaces, and is one of the largest known riverine deposits associated with the terminal MSC. From marked onshore incision and basinward thinning trends, the source of the accumulation is presumed to be a formerly unidentified drainage basin in southern Turkey and western Syria; the deposit extends >500 km into the western Levant Basin, where its depositional sink is marked by six well-developed backstepping lobes. Based on the deposit’s seismic stratigraphy and morphology, which provide clear evidence of subaerial exposure, we question current hypotheses proposing a deep-water origin for late Messinian accumulations. We also draw specific attention to the development of extensive circum-Mediterranean non-marine conditions prior to Zanclean marine transgression, and to the previously overlooked role of fluvial systems in diluting hypersaline lakes in evaporitic basins.