Thousands of Carter's freshwater mussels have died in the Lower Vasse River after a suspected saltwater incursion occurred in the Vasse Estuary.
A Department of Water and Environmental Regulation spokesperson confirmed the deaths after a tip off was received by the Mail.
The spokesperson said that records showed that salinity was detected in the Lower Vasse River in March this year.
"A mussel survey undertaken in April 2021 suggests that there may up to 3,000 mussels impacted. This is based on previous population surveys undertaken in the area where salt water was detected," the spokesperson said.
"It was an unusual event as monitoring records show that the Vasse Estuary and Lower Vasse River have been hydrologically disconnected during summer months for the last 24 years.
"A body of land that normally separates the two systems appears to have washed away naturally last winter allowing seawater to move into the Lower Vasse River in March.
"This erosion combined with a series of unusual weather events combined to connect the two systems."
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Carter's freshwater mussels are a threatened species and listed as vulnerable under the Australian Biodiversity Conservation Act 2016.
The species once spanned from the Gascoyne River to Esperance, but a study published in 2015 titled Range decline and conservation status of Westralunio carteri Iredale, 1934 (Bivalvia : Hyriidae) from south-western Australia found that their range had declined by 49 per cent in less than 50 years.
Salinisation and a drying climate has seen populations of the species reduced to rivers and lakes ranging from Moore River to Waychinucup River.
A DWER spokesperson said the loss of any fauna in our rivers and estuaries was always disappointing.
"The state government agencies, together with the City of Busselton are working to better understand the situation and make any necessary changes to how the system is managed when these type of weather events occur," the spokesperson said.
"DWER are currently monitoring salinity levels in the river weekly to identify if, and when any future saline water incursions take place.
"Current monitoring is indicating that the river is predominantly fresh with low levels of salinity in deeper pools.
"Seawater has been allowed into the Vasse Estuary via the Vasse Surge Barrier since 2015 as a means of reducing algal blooms, reducing the risk of fish kills and reducing offensive smells to neighbours from exposed sediment.
"This year has highlighted the complexity and challenges of managing water levels in the Vasse Estuary to support water quality, ecology and people."