The Messinian salinity crisis (MSC) is an extreme event in Earth history during which a salt giant (>1 × 106 km3) accumulated on the Mediterranean seafloor within ∼640 k.y. Erosional unconformities extending from the continental margins into the deep basins are key features for reconstructing the MSC; however, the nature of the erosional processes and their subaerial versus subaqueous origin are highly controversial. This study focuses on the top erosion surface (TES) in the deep Levant Basin, which is notably flat, truncating a basinward-tilted Messinian evaporitic succession. Based on high-resolution seismic surveys and wireline logs, we show that (1) the TES is actually an intra-Messinian truncation surface (IMTS) located ∼100 m below the Messinian-Zanclean boundary; (2) the topmost, post-truncation Messinian unit is very different from the underlying salt deposits and consists mostly of shale, sand, and anhydrite; and (3) the flat IMTS is a dissolution surface related to significant dilution and stratification of the water column during the transition from stage 2 to stage 3 of the MSC. Dissolution occurred upslope where salt rocks at the seabed were exposed to the upper diluted brine, while downslope, submerged in the deeper halite-saturated layer, the salt rocks were preserved. The model, which requires a stratified water column, is inconsistent with a complete desiccation of the eastern Mediterranean Sea.