The Federal Government has struck a deal with Labor to ensure the Murray-Darling Basin Plan remains intact, easing concerns it was about to crumble without political support.

The Murray-Darling Basin Authority (MDBA) wants to return less water to the environment in the southern basin, saying it needs to balance the need to improve the river's health with the need to protect jobs in irrigation-dependent communities.

But the Federal Greens vowed to stop that with legislation in Federal Parliament, saying it would deny South Australian farmers and the environment of water that was needed.

The Greens spent months lobbying Labor and Senate crossbenchers to support a disallowance motion in the Upper House.

The MDBA warned that if the Greens got enough political support, it could spell the end for the plan and "undermine the food bowl of the nation".

Agriculture Minister David Littleproud said the "historic" agreement would provide clarity to many communities.

"It gives them the certainty of their livelihoods, it gives them the opportunity to get on with their lives without government being in it," Mr Littleproud said.

"Today, Tony Burke and the Australian Labor Party have taken my hand and I thank them for that.

"This shows to every Australian out there, that this place here, we can get outcomes."

New South Wales and Victoria had threatened to walk away from the plan if the Greens succeeded.

Last week, the MDBA urged crossbench senators not to support the Greens, saying it would only make it harder for irrigation communities.

Greens senator Sarah Hanson-Young has accused Labor of selling out the environment and South Australia.

"Doing a deal with the National Party to cut environmental flows in favour of big corporate irrigators says everything," Senator Hanson-Young said on social media.

On Monday, Senator Sarah Hanson-Young said South Australia was being "screwed over time and time again by the plan".

"Last week I was down at the bottom of the river — at the river mouth — it's sick, it's dying and we're not getting the water we were promised coming through the system."

In February, the Greens led a successful disallowance motion to block a reduction in environmental water from the basin's north.

But the party has been unable to secure the same support for the southern basin.

In a statement, Shadow Environment Minister Tony Burke said there were legitimate questions about the northern basin review.

"The best way way to deal with these concerns is through improved transparency, new auditing compliance requirements to ensure a healthy working basin," Mr Burke said.

"Labor has also been determined to make sure that decisions about the volumes required to restore the system to health are determined by the Murray-Darling Basin Authority and do not instead become subjected to the daily amendment of the political process."