Reports released by the Murray-Darling Basin Authority have revealed a surprising cause of decreasing capacity in the Barmah Choke, on the Murray River.
The MDBA has found a massive 'slug' of sand, believed to be caused by gold-mining and land clearing upstream in the 19th and early 20th centuries, has been slowly moving downstream.
It's now accumulating in the Barmah Choke.
MDBA River Management executive director Andrew Reynolds, said the findings highlighted the complexity of managing the river.
"We have been seeing the capacity of the Barmah Choke diminish for some time now," Mr Reynolds said.
"Back in the 1980s, it was about 11,300 ML per day-but now it's about 20 per cent less than that, at just 9,200 ML per day."
He said the MDBA set out to investigate the possible causes of that decrease in capacity.
"What we found was quite incredible," he said.
"A survey of a 28 kilometre 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 the coarse, sandy sediment had 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," he said.
"To understand where it came from, and how it got here, we engaged independent experts who considered a range of hypotheses, including flooding, historical desnagging and regulation of the river system.
"But our analysis found that the most likely explanation is that land-use changes - n particular gold-mining and land clearing - were responsible for introducing large volumes of sediment to the Murray River over a short period of time."
During the gold rush, river channels were used to 'process' huge volumes of sediment, with the gold dropping out into cradles and sluice boxes.
This would have introduced a large pulse of sediment - known as a 'sediment slug' - to the river system.
The slug has been gradually moving through the river - and now appeared to be contributing to problems in the Barmah Choke.
"Capacity through the choke is particularly important for running the river efficiently to meet both consumptive and environmental needs downstream," Mr Reynolds said.
"With less water able to flow through the choke, there is a higher risk of shortfalls - that is, that we won't be able to get water where it's needed, when it's needed.
"There is more work to be done and more for us to learn about this complex problem.
"Importantly, these findings do not change the current trade restrictions for the Barmah Choke - these restrictions will remain in place."
The challenge for Basin governments and communities was how to deal with it, through such an ecologically and culturally important forest.
"Obviously you can't just rashly start dredging the river," Mr Reynolds 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."
He said the MDBA needed 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.
"These findings go to show the complexity of restoring the balance in the river system. In managing the river, we are still seeing the impacts of legacy issues from almost 200 years ago.
"Ensuring a sustainable future for the river is a mammoth undertaking, and it is not something that can happen overnight."
Mr Reynolds said the MDBA would consult with key stakeholder groups on capacity issues and shortfall risks in coming days.