A massive "slug" made of sand has been discovered accumulating in the choke.
The slug is believed to have been caused by gold-mining and land-clearing upstream in the 19th and early 20th century, with the sediment gradually making its way down the river to the choke.
The capacity of the river has been gradually falling over the past 40 years according to Murray-Darling Basin Authority executive director of river management Andrew Reynolds.
“We have been seeing the capacity of the Barmah Choke diminish for some time now,” he said.
“Back in the 1980s, it was about 11,300ML per day, but now it’s about 20 per cent less than that, at just 9,200ML per day.”
Mr Reynolds said in the process of investigating the diminishing water levels the "slug" was discovered.
“A survey of a 28km stretch of river revealed that, for every kilometre of river length, 84,000 cubic metres — or 112,000 tonnes — of sediment was estimated to be on the bed. That’s more than three million tonnes just in the area we surveyed,” he said.
“This coarse, sandy sediment has a very different profile and composition to the surrounding river banks, so it’s pretty clear that it’s not caused by local erosion, and in this part of the river it’s averaging more than one metre deep — with some areas over four metres deep.”
Mr Reynolds said during the gold rush, river channels were used to "process" huge volumes of sediment, with the gold dropping out into cradles and sluice boxes.
It is believed this would have introduced a large pulse of sediment to the river system.
“This slug has been gradually moving through the river and it now appears to be contributing to problems in the Barmah Choke,” Mr Reynolds said.
The issues with the choke could contribute to water shortfalls.
Mr Reynolds said the task was to figure out how best to clear the river.
“Obviously you can’t just rashly start dredging the river,” he said.
“As an independent science-based organisation, what we do must be based on evidence.
“The ecological, economic and community implications of any course of action will be carefully considered, along with input from First Nations peoples.
“We also need to properly understand the longer-term rate of sand build-up and associated loss of channel capacity.
“As directed by basin ministers, we will also be undertaking a feasibility study looking into ways to take pressure off the Barmah Choke, to support system capacity and reduce the risk of shortfalls in water delivery.”
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