Environment Minister Tanya Plibersek said the plan was in "deep trouble" with the next drought just around the corner.
Ms Plibersek said there were three million people who relied on the river system for drinking water and some 30 threatened animal species living across the region.
"If we don't get this right, the environmental impacts are serious," she said.
"We had towns that had bone dry river beds for over 400 days during the last drought.
"We know the psychological, the social toll it took."
The minister has struck a new deal with the NSW, South Australian, Queensland and ACT governments.
It will ensure promised water under the Murray-Darling Basin Plan will be returned to the environment, but over a longer period.
The timeline to recover 450 gigalitres of water earmarked for the environment has been pushed out until the end of 2027 and water infrastructure projects until the end of 2026, after the initial June 2024 target was on track to be missed.
The new plan includes more options and funding to deliver the remaining water, such as through voluntary buybacks.
Victoria is the only basin state to not sign up to the new plan, with the government saying its opposition to water buybacks hasn't changed.
The NSW government said its opposition to water buybacks remained and it wanted to see the Commonwealth prioritise recovering water in other ways.
Water Minister Rose Jackson said the new agreement allowing for more time and flexibility for water infrastructure projects minimised the risk of further buybacks and was a " major motivating factor" for NSW signing up to the new plan.
But South Australian Environment and Water Minister Susan Close said buybacks were the most cost-effective and efficient way to return water to the river.
Ms Plibersek declined to say how much the government would purchase as it could distort the market.
Legislation is set to be introduced to federal parliament later this year.
But Greens senator Sarah Hanson-Young said she wanted a guarantee the water would be delivered this time.
"South Australia is sick and tired of broken promise after broken promise - we want the water the river needs, the environment needs, and we want it locked in."
The 12-year plan to restore the nation's largest and most complex river system, which runs through four states and dozens of towns and cities, was created in 2012 after years of overuse and the devastating millennium drought.
The Murray-Darling Basin Authority has previously advised there would be a shortfall of 750 gigalitres - about one-quarter of the target - by June 2024.
Deputy Opposition Leader Sussan Ley said the new plan was an insult to communities along the river system, saying it would "rip water and rip the heart out of the Murray and Murrumbidgee communities".
"What happens when that water leaves the community?" she told Sky News.
"That farm closes down ... that school comes under threat, doctors don't come to the area because there's not enough community support, infrastructure falls away."
National Farmers Federation chief executive Tony Mahar said water buybacks would lead to higher food and grocery prices and the costs and other impacts were passed on to consumers.
