The old town of Nessebar is near-enough an island: a half mile of weathered wooden fishing houses with terracotta-tiled roofs that sit atop a rocky head, strung to the Bulgarian coast by only a narrow land bridge. It’s also a dense stack of ruins layered on top of one another that stretch back more than 3,000 years, and is recognised by Unesco as a World Heritage site.

When walking into the old town, the twisting streets of 19th-Century fishing houses are parted by the medieval Church of St Stephen – richly decorated with murals of Jesus calming the storm and 1,000 figures from the New Testament – and the excavated ruins of the Stara Mitropolia Basilica, a cathedral dating back to the 5th Century when this was one of the most important Byzantine trading towns on the Black Sea coast.

Archaeologists and local fishermen have found even older relics. A Greek acropolis and pottery date from before the Romans’ arrival, and there are walls built by the city’s founders, the Thracians, the horse-riding warrior people who ruled over the Balkan Peninsula more than 2,000 years ago.

But to find the most surprising artefacts, you’ll need to step off the island and into the surrounding sea.

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Recent oceanographic research efforts using a pair of underwater remote operated vehicles (ROVs) has ventured below the Black Sea waters and revealed pieces of ancient history never before seen in such vivid resolution. These submarine missions have discovered ships from several millennia of seafaring trade and war, including the world’s oldest intact shipwreck: a Greek trading ship from around 400BC lying uncannily well-preserved on the seabed.

And among the wrecks, new evidence offers clues from more than 7,000 years ago, when some experts believe the Black Sea was just a small freshwater lake. Geological samples drilled from the seabed could, at last, settle the mystery of whether it was here that waters once rushed in, flattening civilisations and leaving behind the story we know as Noah and the great biblical flood.

Zdravka Georgieva, maritime archaeologist at Bulgaria’s Centre for Underwater Archaeology in nearby Sozopol, was born on Nessebar and learned to dive in the shallows of the Black Sea. “I really wanted to know what is beneath, what is under the water,” said Georgieva, who first heard about the unexplored remnants of old settlements and shipwrecks at the small Nessebar Archaeological Museum, which holds a smattering of historical artefacts. “I knew from the museum, and from people here, as a teenage girl, that there are historical monuments down there and I wanted to touch them and to observe them really closely.”

After studying at the University of Southampton’s Marine Archaeology postgraduate centre in the UK, Georgieva has been working in her “dream job” as part of the Black Sea Maritime Archaeology Project (Black Sea MAP), which aims to discover how the sea and its surroundings have changed since the last ice age by surveying the seabed.

The Anglo-Bulgarian team, led by Prof Jon Adams from the University of Southampton, in partnership with the Centre for Underwater Archaeology, discovered the 2,400-year-old Greek trading ship last year, in addition to more than 60 wrecks found in deep waters.

Appearing into view as the ROVs 3D-scanned the site, the ancient ship was lying on its side, the mast and rudder clearly visible as well as rowing benches and large ceramic containers in the hold. Georgieva called it “the most spectacular find – so far.”

Georgieva agrees with other marine archaeologists that we are entering a golden age of discovery around the Black Sea.

Archaeologists had known that ancient civilisations had been built here and that ships had traded along the Black Sea coastline. But, until now, imaging technology was not yet advanced enough to provide a true picture of the bottom of the sea, ensuring that anything that lay down there remained shrouded in mystery.

“We knew from historical sources that there had been colonisation of the Black Sea coast, from Greece, from the Mediterranean, but we hadn’t discovered anything like ships. Why? Where are they? What are the reasons we hadn’t found them?” Georgieva asked. “The last four years was a really big step... in how we investigate the submerged landscapes and shipwrecks.”

The fact that remarkably preserved ships can be found here is due to a unique aquatic phenomenon, explained famed deep-sea explorer Dr Bob Ballard.

The last four years was a really big step in how we investigate the submerged landscapes and shipwrecks

Ballard, the American oceanographer best known internationally as the man who led the discovery of the wreck of the Titanic in 1985, has had a decades-long fascination with the so-called “anoxic sea” below the Black Sea: a cold, dead, oxygenless layer blanketed underneath the warm opal waters familiar to visitors.

“I was interested in the anoxia: when I found the Titanic, and we went inside, and saw high states of preservation – the deep sea is a giant museum,” said Ballard in a phone interview from his home in the US state of Rhode Island. As only a few types of bacteria survive in the Black Sea’s anoxic layer, this stasis is strongest here – potentially mummifying human remains and preserving the moments after a disaster in “mint condition” for millennia.

Between 1999 and 2014, Ballard led an expedition to the Black Sea and the Mediterranean that was the first to comprehensively explore this shadow realm. With his crew, he discovered dozens of perfectly preserved vessels, including an Ottoman trading ship that contained human remains.

“It was a good 15-year effort of mounting multiple expeditions, trying to show that the [ancient mariners were] much bolder than historians were giving them credit for – that they pursued direct deep-water trade routes, trying to show that they did not hug the coastline, but chose to go across open ocean.”

But both Georgieva and Ballard said deep-sea exploration provides new clues in another, perhaps even greater, mystery.

In the bestselling 2000 book Noah's Flood by William Ryan and Walter Pitman, marine geologists believed they had found the historical origin of the legends of a great flood that tore through ancient civilisations bordering the Mediterranean and Black Sea 7,600 years ago. Earlier told in the Babylonian creation myth, the Enuma Elish, and in the Mesopotamian Epic of Gilgamesh, the story has become best known across the world in the form told in the biblical story of Noah’s Ark.

According to Ryan and Pitman, about 20,000 ago, what is now the Black Sea was cut off from the Mediterranean by a mountainous landscape.

The Noah’s Flood theory claimed that as Earth’s last ice age ended, melting polar ice caps caused the Mediterranean waters to rise, which pushed a channel through the mountains to form what is now the Bosporus, resulting in a catastrophic seawater deluge 200 times stronger than Niagara Falls. In months, it estimated, the Black Sea inundated a land mass the size of Ireland, flooding a mile a day.

I think you’re going to see the Black Sea yielding a lot of additional chapters of human history now we know where to look

Ballard, in 2000, hoped to shed light on Ryan and Pitman’s theory, when he discovered the pre-flood shoreline, and buildings from human civilisations that lived along it, 12 miles off the Turkish Black Sea coast. He believed these findings would back up the flood hypothesis.

But Black Sea MAP points in a different direction, explained Georgieva. “The geophysicists and other specialists from the oceanographic centre in Southampton, say there’s no evidence to support this theory,” she said. “What we collected doesn’t prove this catastrophic flood. Data shows a more likely gradual sea level rising.”

With more data to be analysed, it supports the idea that the waters rose unnoticeably, by metres over centuries, even millennia.

Still, Ballard calls The Black Sea a “magical place”, an area with “an amazing amount of history”, which has more to offer archaeologists and fans of historical legend than the Noah’s Flood connection. “The Black Sea has that [the biblical connection]; it’s also were Jason and the Argonauts went in search of the Golden Fleece,” he added. “There’s so much more to be discovered in the Black Sea. I think you’re going to see the Black Sea yielding a lot of additional chapters of human history now we know where to look and how to look.”

For locals and visitors, the excitement being revealed offshore does not feel far away.

Bulgaria hosts a richness of archaeological history from Roman, Greek and other ancient societies, the likes of which tourists often seek out in Mediterranean neighbours, Italy and Greece. But here, findings are being unearthed in an accelerated process, especially since 2007 when funding started arriving with Bulgaria’s accession to the European Union.

Nessebar sits on a stretch of coast slightly more than 100km by car from the Bulgarian city of Varna in the north, and nearly 70km from the peninsula of Sozopol in the south, where dense history is laying the foundations for an emerging Bulgarian archaeological trail.

In 2012, nearby Solnitsata, labelled Europe's oldest prehistoric town (albeit controversially) by its discoverers, joined already discovered marvels to the north of Nessebar such as the Varna Necropolis, the oldest gold treasure in the world dating from around 4,500BC, many years before the pyramids of Egypt.

While the Black Sea MAP discoveries are too deep for tourists to visit, scuba diving excursions head down to Nessebar’s original defensive walls from the time of the Thracians, and battleships from World War One and World War Two, as well as the airplane of former Bulgarian Communist leader Todor Zhivkov, which was deliberately sunk in Varna Bay in 2011 to spawn an artificial reef.

To get a sense of what is out at sea, Georgieva recommends that divers visit what she calls the “open museum” of Nessebar’s fortifications, the exposed walls visible on the short walk around the edge of the island, along with similar ruins in Sozopol.

But the discoveries made by the Black Sea MAP team are also being brought up into the light, and are currently on show in Lost Worlds, an exhibition touring Bulgaria where visitors can explore a digital recreation of the 2,400-year-old shipwreck and 3D printed models made from scans of it while wearing virtual reality headsets.

Sunken Civilisation is a BBC Travel series that explores mythical underwater worlds that seem too fantastical to exist today but are astonishingly real.

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