The first shipwrecks linked to the real pirates of the Caribbean in the Bahamas have been discovered by an international team co-directed by a British marine archaeologist.

Blackbeard and Calico Jack Rackham were among pirates who, between the 1690s and 1720s, turned Nassau on the island of New Providence into a hideout where they plotted their next heists on the high seas and divided up their plunder.

Now, following the first-ever official permission to dive in the closed zone of Nassau harbour, an expedition has found six wrecks, three of which can be traced to the “golden age of piracy”.

Pirates were known to destroy evidence of their crimes by setting fire to ships they had seized, having raided their lucrative cargo, cannon and fittings. The archaeologists discovered a charred wooden hull, still weighed down by a stone ballast pile.

Swivel guns, pivot-mounted cannon, were the pirates’ weapons of choice for sparking panic on enemy decks. The archaeologists found what they described as just such as an example – “a calling card of pirate attacks”, they said – along with an iron cannon and a pile of 25 lead musket balls, and a grinding stone for sharpening swords.

The finds have exceeded expectations, because the seabed had been heavily scooped out by dredging.

Dr Sean Kingsley, a British marine archaeologist and the project’s co-director, told the Guardian: “These finds are the tip of the iceberg. I was shocked at the unexpected survival of a wooden hull – ships were the key tool of pirate terror, after all. There could very well be dozens more shipwrecks in and around the harbour.”

Referring to the charred hull, he added: “To actually see and touch it really was a once-in-a lifetime moment and quite emotional.”

In 1695, Henry Avery became the most wanted criminal of his day after he pulled off the most lucrative heist in pirate history, looting gold, silver, sapphires, emeralds and diamonds worth more than £85m in today’s money.

When the archaeologists discovered the charred hull, whose timbers had been connected by wooden treenails, they wondered whether this could have been Avery’s pirate flagship, the Fancy. This one had been burned down to the waterline.

Dr Michael Pateman, the expedition’s co-director and the ambassador for history, culture and museology in the Bahamas, said: “Burning ships to the waterline was an infamous tactic to hide felony from authorities. The Nassau hull shows all the signs of pirate mischief.”

He added: “The ship was heavily armed, especially with swivel guns … Slotted on to deck rails, these anti-personnel weapons raked devastating fire on enemy crews.”

The discoveries are all the more exciting because, while a handful of pirate wrecks have been found between Mauritius and North Carolina, not one had previously been discovered in Nassau, “the home port of the pirates of the Caribbean in the Bahamas”, Kingsley said.

Referring to the $4.5bn Pirates of the Caribbean film franchise, he said: “Thanks to Hollywood, everyone loves the legend. But, beyond the fantasy, nobody knows how the sea dogs really lived … and what happened to the vehicles of their mayhem, wooden ships.”

Kingsley has explored more than 350 shipwrecks in the past 30 years and is the founding editor of Wreckwatch, the world’s only magazine dedicated to the sunken past.

The latest discoveries were made by an international team of archaeologists and film-makers, the New Providence Pirates Expedition – which is dedicated to science, education, entertainment and tourism in the Bahamas – and Wreckwatch TV.

The explorer and project film-maker Chris Atkins spoke of the dangers of this expedition: “Tides flush dangerous currents through its waters twice a day. It’s home to notorious packs of sharks. This was a risky expedition with high chances of finding nothing.”

The waters also have one of the world’s largest concentrations of sharks. “But we didn’t bother each other underwater,” Kingsley said. “We were conscious of respecting their realm.”

The team also discovered rigging, glass bottles and bricks from a ship’s cooking galley still preserved, along with 143 clay tobacco pipes, some of which were sticking out of the sand next to fragments of wooden shipping crates.

The pipes had been decorated with a unicorn, horse, crown and the royal crest of England, suggesting they were made in London around the 1740s.

Kingsley said: “No others have been found in a wrecked cargo. The ship was likely English and sailed for Nassau just after the pirate menace had been crushed. The survival of the wreck, heavily smashed by coastal development, is a miracle. The trader’s cargo of wine in glass bottles and fancy smoking pipes sheds rare light on Nassau becoming a normal port of trade, bouncing back from the pirate anarchy.”

Between dives, the team pored over 300-year-old documents and old maps. They also explored caves where pirates allegedly hid treasure in Nassau. The pirates had taken everything with them, it seems.

The expedition is covered in the first episode of a mini-series, Mystery of the Pirate King’s Treasure, launched this week, as well as the next issue of Wreckwatch magazine.