The plan to save the Murray has been plagued by maladministration with those implementing the rescue disregarding science, failing to account for climate change and almost totally opposed to transparency, South Australia's royal commission investigating the river system has been told.
Senior counsel assisting the inquiry, Richard Beasley, says the Murray-Darling Basin Plan was transformative legislation and had been hailed as ground-breaking reform.
But he says its implementation, at crucial times, has been characterised by a lack of attention to the requirements of the Water Act and a "near total lack of transparency in an important sense".
"The implementation of the basin plan has been marred by maladministration," Mr Beasley said in his final submissions on Tuesday.
"By that, I mean mismanagement by those in charge....and the consequent mismanagement of a huge amount of public funds."
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Mr Beasley said every piece of scientific evidence presented to the investigation, which universally pointed to failures in the plan, had gone unchallenged.
He was critical of the Murray-Darling Basin Authority and other federal government agencies for the failure of officials to give evidence and described a decision by the South Australian government to deny commissioner Bret Walker an extension of time as a "great opportunity lost".
Mr Beasley said the implementation of the basin plan continued to have a negative impact on the environment and probably on the economies of all the basin states.
"But the state that will suffer the most is the state at the end of the system, South Australia," he said.
The commission was also told that the 450 gigalitres of extra environmental flows, to bring the total recovered to 3200 gls and secured largely through SA's lobbying, was "highly unlikely to ever eventuate".
Mr Beasley said the continued extraction of water from the basin had not been based on the best available science, as it was required to be, but rather science that experts suggested had been "trimmed" to produce a politically acceptable result.
He similarly criticised the basin authority's failure to account for the impacts of climate change, describing it as a "glaring omission".
"The MDBA has failed to deal with or engage with climate science in any meaningful way," Mr Beasley said.
Commissioner Walker has spent almost a year examining a wide range of issues associated with the basin and the management plan to ensure the future viability of the river system.
His investigation was launched after reports emerged of widespread rorting and water theft among upstream states.
Mr Walker is due to hand his final report to the state government by February 1 next year.
