The future of the Murray-Darling Basin Plan is at risk after federal government changes which sought to distribute water differently were shot down in the Senate.
The coalition was unable to strike a deal with Labor, which supported a Greens disallowance motion which passed 32 votes to 30 on Wednesday.
"Make no mistake, tonight the Australian Senate puts the Murray-Darling Basin Plan in peril," cabinet minister Simon Birmingham told parliament.
The government was attempting to reduce the amount of water being returned to the environment in southern Queensland and northern NSW, easing pressure on farmers in those regions.
South Australian Greens senator Sarah Hanson-Young said blocking the changes would provide the chance for integrity to be restored to the plan after allegations of water theft in the northern part of the basin.
She believes the changes will hurt communities who rely on the Murray River in SA.
"Big corporate irrigators have been ripping off the river, ripping off the taxpayer, and all this regulation does is reward them," Senator Hanson-Young said.
The two Nick Xenophon Team senators and independent Cory Bernardi, all from SA, also backed the Greens' move to sink changes to the plan.
Labor and the NXT are open to further negotiations, arguing it is up to the government to meet their demands on compliance and environmental concerns.
NXT senator Rex Patrick said his party was willing to support the changes, but not under the current circumstances.
Assistant Water Minister Anne Ruston warned Victoria and NSW government threats to withdraw from the plan were not a bluff.
"If we see an outcome where New South Wales or Victoria choose to walk away from this plan as they've threatened to do, it would be an unmitigated disaster," Senator Ruston said.
She said she wasn't moving away from serious allegations of water theft, but urged her Senate colleagues to work constructively to fix the plan rather than blow it up.
"Stop the blame game. Can we please come back to the table?" the SA senator said.
On Tuesday, NSW and Victorian water ministers, Niall Blair and Lisa Neville, said they would pull out of the basin plan if the Turnbull government's proposed changes were not passed in the Senate this week.
Water has been a hot issue in the South Australian election, where Labor is seeking to retain government.
Australian Associated Press