The state's environmental regulator has ordered Alcoa to urgently flush out the pipeline which crosses the Samson Dam, about 100km south of Perth.
It says the pipeline is likely to contain wastewater contaminated with PFAS, known as "forever chemicals" because they are very slow to break down and are associated with a range of serious health issues.
Alcoa built the pipeline to transfer PFAS-contaminated wastewater to a treatment plant at its Willowdale bauxite mining operations.
It did so despite an application to construct the infrastructure remaining under assessment by the Department of Water and Environmental Regulation.
A prevention notice issued to Alcoa said the construction of the pipeline contravened the department's public drinking water supply protection policy.
It also failed to meet containment measures to prevent the release of PFAS to soil, groundwater or surface waters.
"I consider that a release of PFAS contaminated water through pipeline joints or loss of pipeline integrity to be a real and not remote possibility," a department inspector said in the notice.
"PFAS is highly soluble and highly mobile and has the potential to cause impacts to aquatic ecosystems and human health."
The department further alleged the pipeline had been constructed in locations where it could be easily damaged by site equipment and vehicles.
Alcoa has been given 48 hours to purge the pipeline with clean water to remove any contamination.
It must then deposit the purged water into an authorised waste disposal facility.
An Alcoa spokeswoman said traces of PFAS had first been found at the WA bauxite operations in 2019, prompting the company to stop using firefighting foams containing PFAS compounds and implement testing and containment controls.
The use of a sealed and monitored pipeline was found to be the "safest and most effective" way of transporting the water.
"DWER were informed prior to construction commencing," she said.
"The pipeline was used for a short time in 2022 and has not been used since. It is located in a maintenance corridor that can only be accessed by authorised personnel using light vehicles. There have been no leaks from the pipeline.
"Alcoa has a 60-year history of mining bauxite in the south-west of WA without having any negative impact on public drinking water supply."
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