One of the region's "most pristine" waterways could be under threat from government intrusion, with the state flagging the possible removal of Lennox Weir which stops saltwater from infiltrating Carbunup River.
A saltwater incursion into the Vasse Estuary in May this year was believed to have caused the deaths thousands of threatened Carter's freshwater mussels in the RAMSAR listed waterway.
Carbunup River is home to marron, perch, cobblers and Carter's freshwater mussels. Its surrounding vegetation provides habitat for critically endangered western ringtail possums and black cockatoos.
Potato farmer Vaughan Carter, whose is an adjoining landowner, commissioned a flora and fauna study on the river system for the National Trust which is looking at creating a wildlife corridor along the river.
Mr Carter said when the tide was low mussels were quite prominent, and would be affected if the weir was removed.
"The environmental impact of saltwater going up any further than it is now would be detrimental to the Carbunup River system," he said.
"We have seen the population of mussels devastated in the Busselton river systems.
"When the boards are up at the weir coming into summer, it creates a unique environment for lots of different species of animals including long-neck tortises, freshwater crayfish and of course the mussels."
The heritage listed weir protects the river's freshwater ecosystem and its water has been used by adjoining farmers to irrigate their land for around 100 years.
Mr Carter uses the water source to irrigate his farm and said he would be impacted if the water level was not as high in the river.
"If they remove the weir and I do not have that water source available now, I would have to change my method, that is an impact and that is a cost," he said.
"It is more about the environment for me then what I do as a farmer to be perfectly honest. I can manage what I do in another way, it is more about what the impact will be on the river system and environment.
"There is less than 1 per cent of forested region around Carbunup and Quindalup from what is was pre-European settlement, which is quite significant in the scheme of things."
The government has proposed removing the weir and are waiting on an assessment from the federal Department of Agriculture, Water and Environment before a decision is made on its future.
Water Minister Dave Kelly said Water Corporation had commissioned consultants to examine future options of the weir.
"Lennox Weir was installed in 1928 and comprises a concrete base, metal columns, and a series of removable timber boards," he said.
"It serves no operational function under the Water Services Act 2012 and its condition presents operational and public safety risks.
"The weir has significantly deteriorated due to age, is inoperable, and no longer meets safety standards."
The government estimated it would cost $150,000 to decommission the weir compared to $5 million to replace it.
"Removing the weir stop boards and steel frames may see a short-term, temporary increase of saline water in the upstream during storm surge events, however, this is an entirely natural process experienced in other river systems throughout the region," Mr Kelly said.
Sheep farmer Keith Rose said all they needed to fix the weir was a "bloke with a welder."
"It is a pretty simple fix. It took us three days in 1976 to re-weld bits across the weir. The weir has been there since 1928 and there has never been an accident on it," he said.
Mr Rose said sections of the weir had rusted which needed replacing, which was last done almost 50 years ago.
"They have done it before they can do it again and it will last another 50 years," he said.
Mr Rose said towards the end of Summer the water in the river was a lot lower than sea level and if they pulled the weir out the seawater would run through.
"The weir was put in by the government to keep the seawater out.
"They say we want it kept their for irrigation, that is not the reason at all, we want it kept there to keep the sea out and to keep the sea out we have to put boards in.
"When you put the boards in it creates a storage of freshwater in the river which will benefit farming, but that is not the reason we need the weir.
"We want to keep the river fresh, it is as simple as that.
"Because the water is fresh we get a benefit on the farm which allows farmers to use the freshwater.
"If sea water came into the river it would make all this system useless for farming."
Vasse MLA Libby Mettam said the proposed removal of the Lennox Weir was madness and would have a devastating impact on the ecology of the Carbunup River and its unique and valuable surrounding vegetation.
"The Carbunup River is the most pristine river in the Geographe Bay Catchment fringed with very high conservation value vegetation," she said.
"It makes absolutely no sense to remove the structure that manages the high tide saltwater intrusion.
"Years and millions of dollars have been spent trying to improve the challenged waterways of the Geographe Catchment and Busselton Wetlands and yet the McGowan government is now proposing to cause devastation to this pristine river and its restored and protected riparian environment just to save dollars.
"It will undermine decades of work of GeoCatch and many other agencies including the City of Busselton.
"A study into the Lennox Weir commissioned by the Water Corporation last year was explicit on the need to retain the structure to preserve the ecology of the river and the surrounding old growth and restored vegetation.
"Saltwater intrusion by the removal of the weir will decimate the native flora on the banks, threatening carter mussels, marron and fresh water native fish in the river, and destroy the habitat of possums and cockatoos that live in the surrounding vegetation.
"It will be an environmental disaster. It demonstrates the McGowan Government only pays lip service to environmental sustainability.
"It is essential the Lennox Drain has a structure that can manage the high tide saltwater intrusions that is a growing issue - this should be a government priority."