In 1961, seismic surveys were carried out on the Mediterranean basin. These surveys found a geological feature 100 - 200 meters (330 - 660 ft) beneath the Mediterranean sea floor, dubbed the M reflector. In 1968, the Deep Sea Drilling Project (DSDP) began, supported by Texas A&M University. While bringing up rock cores from the Mediterranean sea floor, the research vessel Glomar Challenger discovered a layer of evaporites (anhydrite, gypsum, rock salt, arroyo gravel) up to 3 kilometers thick. This was certain evidence that the Mediterranean Sea had partially or entirely evaporated at some point in the recent geologic past, during Miocene times, about 5.9 million years ago. This event was thereafter called the "Messinian Salinity Crisis," named after Messinian evaporite discovered on the island of Sicily.

Scientists later pieced together the evidence and determined what happened in the Mediterranean Sea 5.9 million years ago. The Strait of Gibraltar closed on a cyclic basis, at least several times over a 700,000 year period. The layer of evaporites was far too thick to be deposited in a single event. Even today, the Mediterranean Sea is evaporating faster than it is being replenished, due to a lack of large glaciated mountains as a water source and relative disconnection to the World Sea. If these waterways were shut off, the Mediterranean would evaporate dry in only a thousand years.

Although some parts of the Mediterranean are as much as three miles deep, comparable to the deep ocean, the Strait of Gibraltar's depth is about 300 meters (1,000 ft), still very deep, but possibly changeable. 5.9 million years ago, the Eurasian and African tectonic plates would have been closer together, and the strait was likely shallower. Glaciation may have taken water from the world's oceans and lowered the sea level enough to close off the strait. Deeper changes to the underlying crust from tectonic forces may have been at play, such as by changing overall rock density.

The dry Mediterranean basin would have been a lifeless and hot place due to the high salinity and areas of the geography as much as 3 miles below sea level. By comparison, the lowest point on land today, the shore of the Dead Sea, is just 418 m (1,371 ft) below sea level. At 3 miles below sea level, there would be 1.7 times the atmospheric pressure at sea level. This means a wind blowing there would be 32°C to 47°C (57°F to 85°F) hotter here than at sea level, which may have been scorching. The evaporites covering the entire basin would preclude the presence of any plant or animal life. So the dry Mediterranean basin would have been one of the harshest deserts on Earth.