Environment Minister Tanya Plibersek brokered a deal with basin states, excluding Victoria, after it became apparent the government would not hit the water recovery targets slated for 2024.
The plan extends the timeline and introduces the options of voluntary water buybacks, which some states and the federal coalition oppose because of the impact it could have on access and the price of water.
Water buybacks allow farmers to sell their water directly to the government.
Concerns about buybacks stem from the impact the government entering the market can have, including inflating prices when water is withheld in favour of selling to the Commonwealth and supply is cut.
This then flows on to the price of food by increasing the overhead cost of farming if the price of water becomes more expensive.
The 12-year plan was put in place to restore the water levels of Australia's most complex river system, which flows through four states and dozens of towns and cities, after years of overuse and the devastating millennium drought.
Negotiations have now been left to the Greens to pass the plan, which the government wants to be ticked off this year.
Two crossbenchers will also be needed for the bill to pass the Senate.
Negotiations with the Greens are continuing, but Senator Sarah Hanson-Young has been adamant the minor party would not just rubber-stamp the new plan.
The South Australian has called for stronger oversight to ensure the 450 gigalitres earmarked for the environment are recovered. She also wants incremental targets up until the December 2027 deadline.
"We are willing to work with the government to improve this bill, but in its current state it does not deliver the assurances that South Australia or our river needs," she told AAP in a statement.
Ms Plibersek told parliament it was critical the water from the environment was delivered, and that her policy was sensible and balanced.
Environmental groups have welcomed progress on delivering the plan, saying voluntary buybacks provide the opportunity to recover water.
But the Nationals say the buybacks could end up hurting the environment and the communities the basin plan is meant to help, by taking water away from where it is needed most.
The farming lobby also hit back, saying the government had abandoned a commitment to ensure no communities were left worse off by supporting voluntary water purchases.
The Nationals have resolved to bring forward a review of the plan with the aim of developing a "practical water management plan", instead of resorting to buybacks.
Opposition water spokeswoman Perin Davey said the coalition remained committed to delivering the plan without stripping away the social and economic viability of regional communities.
"These amendments rip up that bipartisan support for communities," she told AAP in a statement.
A separate Senate inquiry examining the plan will report in November.
Senator Davey's push to have the inquiry hold public hearings in five basin communities to hear evidence from people impacted by the policy was rejected by the government and the Greens.
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