The flagship of the controversial Sea Shepherd Conservation Society now sits at the bottom of Shelburne Harbour.

On Wednesday port staff noticed MV Farley Mowat was taking on water and called authorities.

By 1:30 a.m. on Thursday, the ship had slipped below the surface, causing concern among local officials whose thoughts have now turned to the clean-up.

"My personal concern is the pollution in the harbour the sea life… We have wonderful marine life there and that's my first concern, protecting that,” said Shelburne Mayor Karen Mattatall.

MV Farley Mowat arrived in the port last September, and has been a rusted eyesore on the waterfront ever since.

It garnered controversy well before that, playing a significant role in the Sea Shepherd’s campaign against the seal hunt.

In 2008, federal authorities seized the ship and towed it into Sydney Harbour after its captain ran into legal troubles.

It was later sold but remained the subject of more battles over unpaid docking fees.

Now, as the clean-up begins, it’s the 37 litres of various products that are aboard the ship, and now underwater, that are causing concern.

“We put about 600 feet of boom around the vessel,” said Canadian Coast Guard senior response officer Keith Laidlaw.

“There is still sheening coming from the vessel. We’ve had Transport Canada 950 surveillance plane fly over the area … to get a good picture from the air of how extensive the pollution is,” he said.

Dylan Heide, Shelburne’s chief administrative officer, says there are other causes for concern too.

"The sunken vessel now presents a hazard to users of the port and really any users of the Shelburne Harbour,” he said.

There is no word on how long the clean-up and salve could take.

The ship is currently owned by Tracy Dodds of Halifax.

With files from CTV Atlantic’s Marie Adsett