The Mediterranean Basin may have not always been connected to the Atlantic Ocean. During the Messinian Salinity Crisis (5.96–5.33 Myr), the Mediterranean Sea reduced progressively its connection with the global Ocean by a complex combination of tectonic and glacio-eustatic processes. During this period, deep erosion occurred on the margin and on the continent. Furthermore, a large quantity of evaporites was deposited in the basins (>1500 m). The way by which the evaporites accumulated in the various sub-basins has not been precisely determined. Here we demonstrate by quantitative analysis that a combination of several Mediterranean sea-level drawdown events associated with limited Atlantic sea inflow and continuous river discharge can explain the quantity of evaporites in the Mediterranean Basins and the observation of an intermediate lowstand at ∼500 m. Using a paleogeographical reconstruction and a numerical model, we show that the evaporites of the Gulf of Suez (GoS) are a consequence of the threshold which disconnected the GoS/Red Sea from the Eastern Mediterranean at the end of the Miocene.