The serene turquoise waters of the Mediterranean Sea hide a sharp-tasting secret: a layer of salt up to two miles thick, lurking deep underneath the basin. The ghostly white minerals are one of the few traces of an ancient Mediterranean Sea that vanished millions of years ago. Some scientists believe that the entire sea evaporated for a time, desiccated like the Sahara to the south.

Even after decades of study, the details surrounding the sea’s vanishing act and the torrents of water that refilled the basin remain an enduring mystery. The refilling of the Mediterranean about five million years ago may have been the biggest flood in our planet’s history. By one estimate, the cascade of water that filled the cavernous basin was about 500 times larger than the flow of the Amazon River.

“It was a sensational thing,” says Daniel García-Castellanos of the Institute of Earth Sciences Jaume Almera in Spain. In a recent analysis published in Earth-Science Reviews, Garcia-Castellanos and his team identified a pocket of sediments that may have been deposited by the megaflood.

Without this cataclysmic reconnection with the Atlantic Ocean, the Mediterranean as we know it today would not exist. Ships couldn’t have crisscrossed the watery highway to fuel the rich cultures that have dotted its shorelines since the early stages of human civilization. And today, the Mediterranean Sea is a vital pump for global water circulation. Evaporation infuses its waters with an extra dose of salt, which spills into the Atlantic and helps drive oceanic conveyor belts that circumnavigate the planet, influencing temperatures, storm patterns, and more.

As modern temperatures continue their steady march upward, and the ice caps dwindle at the poles, it's "pretty blooming important" to figure out what processes led to the planet we see today, says Rachel Flecker, a geologist at the University of Bristol.

The flood of the eon

Today, the Mediterranean Sea’s million cubic miles of water are constantly evaporating, with roughly four feet of water turning to vapor each year. Rains and rivers aren’t enough to sate the system. The only water source keeping the body stable is a steady flow from the neighboring Atlantic Ocean, pouring through a narrow channel between Spain and Morocco, the Strait of Gibraltar.

Many millions of years ago, tectonic shifts deep below the surface may have forced the landscape upward, crimping the vital connection between the Mediterranean and Atlantic. Waters likely continued to flow into the basin, but the shift would have severed the escape route for dense saline currents running along the basin floor to reach the open ocean. Roughly six million years ago, salts began to pile up—enough to give each of the world’s 7.7 billion people nearly 50 Great Pyramids of Giza filled with the stuff.

Some researchers suggest the region nearly dried up before the flood, leaving a cavernous basin dipping more than a mile below current sea level. All that stood between the empty basin and the mighty Atlantic may have been a narrow spit of land where the Gibraltar Strait is today (though the exact width of this former land bridge is still uncertain).

Some 5.3 million years ago, a massive flood breached the divide and reconnected the ocean and the sea. But just as the extent of the Mediterranean’s drying is debated, so too is the size of the flood. With scant evidence available, García-Castellanos and his team wondered just how fast an empty Mediterranean basin could refill. The breach likely started as a trickle over the natural dam connecting modern-day Europe to Africa, according to their models from a 2009 study. But erosion quickly took over. “The process becomes unstoppable very soon,” García-Castellanos says.

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As the water mounted, it scoured out a deepening path that allowed still more water to pass. At its peak, the flow may have gushed at 100 million cubic meters per second, filling the sea in two years or less. Such an event would have excavated at least 400 million olympic swimming pools worth of sediment, cutting a channel through the Strait of Gibraltar and carving a canyon that extends into the seafloor.

“This is like water coming out of a firehose,” says Columbia University’s William Ryan, a marine geologist at Columbia University who was part of early work identifying the Mediterranean salt deposits.

The cataclysmic event transformed the entire region, moving not just water but also cutting away chunks of rock, sand, and anything else in the way. “When you have that kind of energy, you don’t move sediment as little grains bouncing along the bottom. Everything is thrown up into a chaotic, highly turbulent state,” says Victor Baker, a geologist with the University of Arizona and an expert in very big floods.

Piecing together a prehistoric mystery

Geologists of the 1800s didn’t think floods of this scale were even possible. They required evidence from modern processes to prove an ancient event could have occurred. “The problem is, big, giant floods are rare,” Baker says. Similar to the catastrophic Chicxulub asteroid impact that forever changed life on Earth, megafloods don’t happen every year—or even every million years.

Scientists first began digging into the history of the Mediterranean as early as the 1950s, when they found salt deposits on the shores hinting at a particularly briny ancient sea. In the 1970s, researchers on board the Glomar Challenger drilled cores from the seafloor, allowing them to finally lay eyes on the salty remains of this tumultuous time in the sea’s history.

Features that resembled the cracked surface of a mudflat when left to bake in the sun were found embedded in the upper layers of salt—a hint that waters may not have always been sloshing above, Ryan says. But exactly how much of the Mediterranean’s water disappeared, and for how long, remains hotly debated.

Over the years, many researchers have dipped their toes into the puzzling waters, and as more evidence accrues, the more perplexing the situation becomes. Throughout the basin, fossils of critters can be found that point to a Mediterranean nearly full of water just before it reconnected to the Atlantic, says Wout Krijgsman, a geologist at Utrecht University in the Netherlands. Perhaps before the flood swept in, the region was not a desert but a shrunken sea.

One of the major questions that García-Castellanos and others have worked to answer is, where did all the sediment go? An estimated 240 cubic miles of sediment would have been strewn across the Mediterranean basin, collecting in pockets where the water flow was low. But the sediments, laid long before people first set foot in the region, are now buried beneath the seafloor.

To spot the ancient clues, researchers use a method akin to a geologic ultrasound, sending seismic vibrations from a boat to the bottom of the Mediterranean and measuring the echoes. A pocket of rocks and sand, possibly deposited by the flood, was discovered just to the east of the boundary that divides the western and eastern basins. And by looking through old seismic data, García-Castellanos and his colleagues think they’ve found another sediment deposit in the form of a rocky tail extending behind a submarine volcano. While the pockets of sediment are intriguing finds, they have not been sampled, so scientists don’t know exactly when they formed, Flecker says.

Yet answers may soon be on the horizon. Flecker and others hope to drill multiple sites throughout the Mediterranean in search of more clues to these key moments in the region’s geologic past.