Scientific testing has shown levels of toxic firefighting chemicals in the waters of popular swimming and fishing area Cockburn Sound are safe for recreational users, according to the inlet's management board.

There were concerns the sound may have been contaminated after it emerged firefighting chemicals used at Australian defence bases may have affected the surrounding areas.

Garden Island, off the WA coast, is home to HMAS Stirling, prompting the Department of Environmental Regulation to test for contamination last year.

But Cockburn Sound Management Council chairperson Kateryna Longley said summer water sampling revealed no evidence chemical contamination at the HMAS Stirling naval base had affected the water quality of the sound.

Dr Longley said the results from 18 sites showed concentrations of perfluorinated chemicals, contained in firefighting foam used at the base until 2004, were at or below the health guidelines.

Defence to carry out own tests

The news comes as the Department of Defence confirms it will sink its own bores in beaches around the Garden Island base to determine just how far the chemicals have leached into groundwater.

Australian Navy's Rear Admiral Clint Thomas says his department believes it is safe to swim in the sound. ( ABC News: Rebecca Turner )

This will be part of its extensive one-year environmental investigation, sparked by findings released last November that many bores on the island were contaminated at levels higher than Australian drinking water guidelines.

Defence spokesman Rear Admiral Clint Thomas said his department believed it was safe to swim in Cockburn Sound, but the inquiry would provide the scientific evidence to reassure locals.

"We will sink bores in and around the beaches, in and around the high-water mark," he said.

"The consultant will be taking samples of sea life, seaweed, seabed sediment, et cetera.

"I have no doubt that by the end of this process we will know what the concentration levels will be on the island and in the near vicinity of the island."

Drinking water main concern

Rear Admiral Thomas, who ran two information sessions today for people living around Cockburn Sound, said the investigation would take a year and be conducted by consultants RPS Environmental.

HMAS Stirling is one of at least 13 Department of Defence sites around Australia — including the RAAF air bases at Oakey in Queensland and Williamtown in New South Wales — which are being tested for contamination by the toxic chemicals contained in firefighting foam.

Since the early results of testing at HMAS Stirling were released last November, the Australian guidelines for safe exposure to perfluorinated chemicals in drinking and recreational water have been dramatically reduced.

As a result, some HMAS Stirling bores considered within safe levels in the November report now exceed the guidelines for drinking water, while another has recorded contamination almost 900 times higher than the levels recommended by Food Standards Australia New Zealand.

But Rear Admiral Thomas said HMAS Stirling was considered a low-risk site because it was an island and its bores were not used for drinking water.

"That is the major risk to human health, the ingestion via bores or through drinking water. The major risk has been mitigated already," he said.