Before what was described as a heated meeting of the Murray-Darling Basin Ministerial Council in Adelaide on Friday morning, Mr Hunter called on the Prime Minister to sack his deputy, Barnaby Joyce.

"We saw what happened in the millenium drought. It's beyond shameful that upstream politicians would even consider consigning the South Australians to the same fate in the future," said Mr Hunter.

Without extra water, the mouth of the Murray would dry up, he said.

Mr Joyce, the acting Prime Minister, told Mr Hunter by letter on Thursday that the government couldn't fulfil his promise in October 2015 to deliver more water "in full and on time".

The dispute became public before an announcement by the Murray-Darling  Basin Authority on Tuesday. The authority is expected to propose changes to the 2750 gigalitres of water recovered from irrigators for environmental flows – including reductions to the northern basin in NSW.

In the leaked letter, Mr Joyce admitted the government could not honour its promise under the plan to deliver additional water to South Australia to keep the Murray flowing.

Emotions were already high at a dinner meeting on Thursday night between state ministers and Mr Joyce before Friday's meeting.

The Weekly Times claims that Mr Hunter swore at Ministers, including Victoria's Water Minister Lisa Neville.

Ms Neville said in a statement that it was a robust discussion, and she didn't "shy away from standing up for Victorians and what's best for our state."

"My South Australian counterpart and I shared different views," she said.

Under the current plan, 2750 gigalitres a year is being recovered from irrigators. But the government had agreed to give the states an additional 450 gigalitres – of which 36 gigalitres would be recovered from South Australia – if they identified ways to reduce water going to farming.

Mr Joyce wrote he could not foresee the other states agreeing to deliver the water without significant social and economic detriment.

The opposition seized on the leaked letter as proof the federal government wasn't going to honour the plan. 

After the meeting, Mr Joyce said he wasn't reneging on the plan, but simply acting in accordance with the legislation which bans the recovery of additional water if it causes significant social and economic detriment.

In NSW, environmentalists and graziers near the Macquarie Marshes also fear that a planned reduction of environmental flows could see the number of birds nesting fall even further.

Sources say the Murray-Darling Basin Authority will on Tuesday recommend a reduction of between 70 gigalitres and 130 gigalitres (equivalent to about a quarter of the water in Sydney Harbour) a year in the northern basin's environmental flows. This was supposed to have returned about 390 gigalitres of water a year from irrigators to the Northern Basin including the Macquarie Marshes - with about 143 gigalitres trickling downstream.

In the middle of what should be a bumper bird breeding season after the flooding in NSW and southern Queensland, waterbird numbers are down across many areas, according to this year's 34th annual Eastern Australian Waterbird Survey by University of NSW's Centre for Ecosystem Science. In the marshes, only six of the 20 traditional breeding sites are active.

"There were more than 100,000 pairs before irrigation; now it might be only 30,000 nesting pairs, and this is supposed to be a big flood," said the centre's Richard Kingsford this week.

Like the thousands of waterbirds he tracks every year, Professor Kingsford migrates annually to NSW's Macquarie Marshes to witness a "great sight of nature: tens of thousands of waterbirds breeding in wetlands".

For 31 years, the scientist has flown over the wetlands, where thousands of egrets, ibis and spoonbills nest in dense colonies, as part of an annual aerial survey to estimate the abundance of waterbirds in eastern Australia.

He's passionate and poetic. The marshes were a "mosaic of thousands of little mini habitats", filled with insects, frogs and reptiles, he said.

Surrounded by reed beds, river red gums and coolibah trees, the birds create a cacophony of sound. Professor Kingsford has watched straw-necked ibis mow down a swarm of locusts in minutes.

Local farmers, environmentalists and scientists say this great sight – only witnessed after flooding streams water across the plains – is fading fast.

They fear for the future if the Murray-Darling Basin Authority proceeds with a plan to reduce the amount of water flowing into the wetlands.

Professor Kingsford likens the marshes to a very ill patient who has been given just enough care to get out of the ICU.

"When I see the dead trees, hundreds of years old; when I see the bird breeding event not as high; when I see our predictions of the long-term impacts of river regulation ... It's obviously still an incredible place but not the same as it used to be," he said.

"The extra flows got it out of ICU, but it will remain compromised without its lifeblood – water. It will never be the same, but we still want something of its former majesty. "

Since irrigation began, and the Burrendong Dam was completed in 1967, it is estimated that the amount of water flowing into the marshes has almost halved.

Even less may come to the wetlands in future. One hundred-year-old river red gums are dying, too, and strawnecked ibis numbers are down.

"Floods create a food bonanza for frogs, insects and reptiles that form a food web for these birds and allow them to breed in large numbers," Professor Kingsford said.

When the floods stop, or occur less often, the birds breed less often. Research by Professor Kingsford and others estimates the number of nests have dropped by 100,000 every 11 years.

This year, the night herons have abandoned one of their favourite nesting strongholds because of a lack of water. Glossy ibis are hard to find.

Ecosystem threatened

Nearly 90 per cent of the marsh is privately owned by graziers, such as fourth-generation farmers Garry and Leanne Hall.

The Halls, who own a 5500 hectare mix of marshland and grazing land, have witnessed a massive reduction in egrets, ibis and spoonbills.

"Total volume has been reducing and it is the future that worries us.  Our expectations are becoming smaller," said Mr Hall, whose family grazes black Angus cattle.

"Water is the key driver of eco system function in a wetland, and  the less water, the less birds, the less bugs, the less bacteria in our soil. It distorts the whole ecosystem, which includes cattle production, and when the dry is longer, we sell less beef."

Local Indigenous groups representing the northern basin are also alarmed by the threat of less water flowing into the region, and have called for an increase.

Jonathan La Nauze, of the Australian Conservation Foundation, said water had been overallocated to industrial and human use in every river system in the Murray-Darling Basin, something that had been recognised by former prime minister John Howard when he announced the creation of the authority nearly 10 years ago.

"If the rumours are true, people charged with that responsibility to address water allocation are going to head in the opposite direction, the first people since John Howard to increase water allocated to irrigation."

The Murray-Darling Basin Authority would only say the proposed amendments would be made available on Tuesday, followed by an 11-week consultation period.

It has foreshadowed changes to the northern basin water recovery target and some groundwater water recovery targets. Sources said representatives of the Murray-Darling Basin Authority have argued they overestimated how much water the marshes needed, and it is expected that they will propose that some of this water should be sold to irrigators upstream.

"The MDBA is currently consulting with basin governments to finalise a proposal concerning the northern basin water recovery target that balances the needs of communities, industries and environment in securing a healthy and productive basin for future generations," the authority said.