Canada's east coast navy is preparing to battle an infestation of marine borers. (CBC)

The $300 million sewage treatment system in Halifax Harbour is now keeping the water clean, but that is causing new problems for the Canadian navy.

Capt. Brian Santarpria said wood-eating organisms called marine borers are thriving in the clear water.

"As the harbour gets cleaner, you get infestations of these marine life that can eat wood," he said Wednesday.

The organisms, also known as shipworms, can eat wooden piers and slipways.

CFB Halifax staff are looking at excavating under wooden pilings, pressure washing them and then wrapping them in four coats of fiberglass to repel the marine borers.

Santarpria said the pollution that had plagued the harbour for decades had also suppressed the organism.

Threat assessment

Canada's west coast naval base at Esquimalt, B.C., had the same infestation, as did U.S. bases along the eastern seaboard.

That prompted the Halifax base to order an assessment as the water cleared up.

"We wanted to know what the threat was," Santarpria said.

The assessment confirmed the presence of the borers. The navy will take 30 days to assess the findings before seeking solutions.

"We're way out in front of this," Santarpria said. "I'd rather have that problem than the reverse."

The navy is not the only big property owner on the Halifax waterfront.

The Nova Scotia government operates three kilometres of wooden boardwalk and wharves along the harbour and Murphy's on the Water uses the waterfront, too.

Peter Murphy, one of the owners, said they are prepared to live with the wood borers.

"We'd rather fight those guys than the other stuff that was floating in the harbour," he said.