The Messinian Salinity Crisis resulted from desiccation of the Mediterranean Sea after its isolation from the Atlantic Ocean at the end of the Miocene. Stratal geometry tied to borehole data in the Gulf of Lions show that the pre-crisis continental shelf has been eroded during a major sea-level fall and that sediments from this erosion have been deposited in the basin. This detrital package is onlapped by high amplitude seismic reflectors overlain by the “Messinian Salt” and the “Upper Evaporites”. Towards the shelf, the transition between regressive deposits and overlying onlapping sediments is characterised by a wave-ravinement surface, suggesting that a significant part of the onlapping reflectors and overlying Messinian Evaporites were deposited during a relatively slow landward migration of the shoreline. The clear boundary between the smooth wave-ravinement surface and the subaerial Messinian Erosional Surface observed on the Gulf of Lions shelf and onshore in the Rhône valley is interpreted to have resulted from a rapid acceleration of the Mediterranean sea level rise at the end of the Messinian Salinity Crisis. Numerical simulation of this cycle of sea level change during the Messinian Salinity Crisis and of precipitation of thick evaporites during the slow sea level rise shows that this scenario can be modelled assuming a value of evaporation minus precipitation of 1.75 m3/m2/yr in the deep Mediterranean basins.