The Mediterranean Basin has not always been connected to the Atlantic Ocean. During the Messinian salinity crisis (MSC), the Mediterranean Sea became progressively isolated by a complex combination of tectonic and glacio-eustatic processes. When isolated, the Mediterranean water level depends on the hydrological flux and is expected to vary significantly. The amplitude and number of large water level fluctuations in the isolated Mediterranean is still controversial, despite numerous geological investigations. The observation of 3–5 surfaces of erosion in the Nile delta (Eastern Basin) provides new elements for understanding the dynamics of the MSC. Our model demonstrates that numerous water level falls of short duration may explain the preservation of a discontinuous river profile at ∼−500 m and ∼−1500 m in the Western Basin, as well as the existence of deep surfaces of erosion in the Eastern Basin.