The head of the Murray-Darling Basin Authority (MDBA) has said the historic agreement to protect Australia's iconic river system for the environment and agriculture is in danger of collapse.

Key points: MDBA chief concerned NSW and Victorian governments will walk away from plan

MDBA chief concerned NSW and Victorian governments will walk away from plan ALP announced it would support Greens' bid to block a cut in the amount of water being returned to northern basin

ALP announced it would support Greens' bid to block a cut in the amount of water being returned to northern basin MDBA said cut would save 200 jobs in irrigation-dependent communities in NSW and Queensland

MDBA chief executive Phillip Glyde told the ABC he was concerned the New South Wales and Victorian governments might act on their threats to potentially walk away from the Murray-Darling Basin Plan.

"It's certainly under a lot of pressure at the moment," he said.

"If it [the plan] does collapse, we go back to circumstances before 2012 where various state governments use water as they may wish, but it doesn't look after the basin as a whole.

"It would undermine the food bowl of the nation, undermine us having a sustainable basin that is environmentally sound."

The crisis was sparked when Federal Labor announced on Tuesday it would support the Greens' bid to block a 70-gigalitre cut in the amount of water being returned to the environment in the northern basin.

The cut, supported by the Federal Government, was recommended by the MDBA, which said it would save 200 jobs in irrigation-dependent communities in NSW and Queensland.

NSW Water Minister Niall Blair said his Government was "deadly serious" about reconsidering its commitment to the plan.

He said the processes built into the basin plan for adjusting irrigation and environmental flows had been agreed to by all of the state and federal governments involved.

"But now, because outcomes don't meet political desires or wants, some want to overturn the umpire's decision," he said.

"We're really questioning whether we would bother with any of the other implementation of the plan, if it's going to be treated like this.

"The hard work that's been done bringing communities along for the difficult conversations, to then have it just thrown onto the scrapheap like this, I don't know, we'd want to be in a position to put our communities through that again."

But tensions are set to rise even further when Parliament considers the potential return of 605 gigalitres of water to communities in the southern part of the basin.

The MDBA said that was linked to greater water efficiencies, which would allow the same environmental benefits for less environmental flows, Mr Glyde said.

The Greens, however, have said they would also move to disallow that.

"All governments have signed up to that 605-gigalitre adjustment six months ago. If that was to fall over I think that would be the end of the basin plan," Mr Glyde said.

"[That's] because that method means we can achieve the environmental outcomes of the basin plan with much smaller economic impact."

A spokeswoman for shadow water minister Tony Burke said Labor would have to read the fine print of any new Greens motion and take it to Caucus before deciding whether to support it.