Scientists are working to conserve a critically endangered species of marron which is only found in the Margaret River in Western Australia's South West.

The hairy marron, a type of freshwater crayfish, is concentrated in the Canebreak Pool area of the river but is under threat from the more commonly found smooth marron.

The smooth marron was introduced into nearby private dams and quickly spread, according to Cape to Cape Catchments Group chair Boyd Wyke.

"With the smooth marron being brought in, probably for people with dams and for growing some marron to eat, they've proved to be interbreeding and competing with the hairy marron," Dr Wykes said.

"There's a possibility that climate change, change in condition of the river might have favoured the smooth marron, but that's fairly speculative at this stage."

Scientists have been moving smooth marron to other parts of the Margaret River in a bid to protect the critically endangered hairy marron. ( ABC News: Roxanne Taylor )

Water Department scientists have been monitoring the health of the river, which supplies some local farm irrigation, and moving smooth marron to other parts of the river.

The Margaret River is linked to the groundwater feeding the Leederville Aquifer which supplies some of WA's drinking water.

Department regional manager Adam Maskew said it was important to ascertain whether the drying climate was affecting the marron's habitat.

"This snapshot will allow us to see whether we need to change those sharing laws to protect the species that are important to us," he said.

Authorities said it would take some time to see the rewards of their work in giving the hairy marron a fighting chance.

"You'll see very little ... you'll just start to get on top of it and all of a sudden the hairies will start to dominate again," Water Department river science manager Tim Storer said.

"[But] it's certainly an effort well worthwhile."