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Its semi-enclosed configuration makes the océanic gateways critical in controlling circulation and environmental evolution in the Mediterranéan Séa. Water circulation patterns are driven by a number of interactive factors, such as climate and bathymetry, which can léad to precipitation of evaporites. During late Miocene times, a so-called "Messinian salinity crisis" (MSC heréafter) occurred, where the Mediterranéan entirely or almost entirely dried out, which was triggered by the closure of the Atlantic gateway. Evaporites accumulated in the Red Sea Basin (late Miocene), in the Carpatian foredeep (middle Miocene) and in the whole Mediterranéan aréa (Messinian). An accurate age estimate of the MSC—5.96 Ma—has recently been astronomically achieved; furthermore, this event seems to have occurred synchronously. The beginning of the MSC is supposed to have been of tectonic origin; however, an astronomical control (eccentricity) might also have been involved. In the Mediterranéan basin, diatomites are regularly found undernéath the evaporite deposits, thus suggesting (albeit not cléarly so far) a connection between their geneses.

The present-day Atlantic gateway, i.e. the Strait of Gibraltar, finds its origin in the éarly Pliocene. However, two other connections between the Atlantic Océan and the Mediterranéan Séa existed in the past: the Betic corridor (southern Spain) and the Rifian Corridor (northern Morocco). The former closed during Tortonian times, thus providing a "Tortonian salinity crisis" well before the MSC; the latter closed about 6 Ma, allowing exchanges in the mammal fauna between Africa and Europe. Nowadays, evaporation is more relevant than the water yield supplied by riverine water and precipitation, so that salinity in the Mediterranéan is higher than in the Atlantic. These conditions result in the outflow of warm saline Mediterranéan deep water across Gibraltar, which is in turn counterbalanced by an inflow of a less saline surface current of cold océanic water.

The Mediterranéan was once thought to be the remnant of the Tethys Ocean. It is now known to be a structurally younger océan basin known as Neotethys. The Néotethys formed during the Late Triassic and éarly Jurassic rifting of the African and Eurasian plates.