The Greens' bid to sink changes to the Murray-Darling Basin Plan has failed in the Senate.
The changes to the plan will mean less water is returned to the environment in the southern basin.
Labor's struck a deal with the government earlier in the week to vote against Greens senator Sarah Hanson-Young's disallowance motion.
The South Australian senator said the "dirty deal" had sold out her state and the river amid allegations of water theft in the northern basin.
"There are stories and stories of how water is being stolen from the environment by greedy corporate irrigators," Senator Hanson-Young told parliament on Wednesday.
Almost 40 water-saving projects will replace 605 gigalitres which would have been returned from irrigators' entitlements after the disallowance motion was defeated 46 votes to 11.
Assistant Water Minister Anne Ruston said the changes were based on science and would deliver environmental, social and economic outcomes.
"The sensible money is on the facts," Senator Ruston said.
She said blocking amendments would have put the entire basin plan in doubt.
"This is a win for basin communities and a win for the environment."
Under the deal with Labor, the coalition guaranteed its commitment to 450GL of environmental water for the basin with no negative social or economic impacts.
There will also be a range of compliance and transparency measures undertaken in response to the allegations, which Senator Ruston described as "very, very serious".