Many mysteries lie below the surface of the sea, including a large shipwreck found at the bottom of a Nova Scotia harbour.

The mystery begins in Pictou Harbour, where last month the Canadian Hydrographic Service found something unusual while updating navigational charts.

“The interesting part of this is that it wasn't on the charts,” says Jon Griffin, of the Canadian Hydrographic Service. “Most likely, owing to the fact that the technology of the time wasn't sufficient to capture the detail.”

That detail, using acoustic sonar and 3D imagery, is amazing. It shows a ship, 84 metres long and 17 metres wide, lying at the bottom of the harbour.

“The boat is in about twenty feet of water. The vessel appears to be intact, like it’s not broken in half and there's a gap in the middle. I can see that much,” says Griffin. “It's on the edge of the channel and the boat is without any superstructure. There's no rigging. There's no house. The boat appears to be just sitting intact, on the bottom.”

It's not known how old the boat is, what it’s made of, or even what kind of vessel it is. That lack of knowledge has led to plenty of speculation and interesting stories.

Historian Clyde MaCDonald has a favorite story, about a boat called The Favorite, that sailed from Scotland to Pictou in 1802.

“And as soon as the 500 passengers were taken off the ship and all of the cargo was taken out of the ship, the ship sank,” says MacDonald. “Rollie Sherwood, a noted historian from Pictou, stated in his book that it was witchcraft. That this is what caused the ship to sink.”

The wreckage will be marked on marine charts, and further answers about the boat, may not be far off.

“We have a camera here that we are going to, as time and opportunity permits, drop a camera over. The water's awfully murky. I have no idea what we'll see,” says Griffin.

One thing that is certain is that the mystery vessel is not the Ship Hector. The original was lost off the coast of the United States centuries ago and the replica still sits at the Hector Heritage Quay.

With files from CTV Atlantic's Dan MacIntosh