The Murray-Darling Basin Royal Commission has found Commonwealth officials committed gross maladministration, negligence and unlawful actions in drawing up the multi-billion-dollar deal to save Australia's largest river system.

Key points: The royal commission started after an ABC investigation into NSW irrigators

The royal commission started after an ABC investigation into NSW irrigators Royal Commissioner Bret Walker said the MDBA was "unwilling or incapable of acting lawfully"

Royal Commissioner Bret Walker said the MDBA was "unwilling or incapable of acting lawfully" He accused the original architects of the plan of being driven by "politics rather than science"

Commissioner Bret Walker SC recommended a complete overhaul of the Murray-Darling Basin Plan, including reallocating more water from irrigation to the environment.

The 746-page report, which made 111 findings and 44 recommendations, found the original plan ignored potentially "catastrophic" risks of climate change.

The investigation into the Murray-Darling Basin Plan, prompted by allegations of water theft by NSW cotton farmers which first aired on Four Corners in 2017, recommended major reform including resetting water saving limits, repealing the outcome of the Northern Basin Review and new measurements for water on flood plains.

The plan, signed into law in 2012 by basin states and the federal government, aimed to remove 2,750 gigalitres (GL) of water through irrigated agriculture and return it to the river system to help the environment.

Commissioner Walker accused the Murray-Darling Basin Authority (MDBA), the body responsible for implementing the reforms, of failing to do so.

"Regrettably, from prior to the time of the enactment of the basin plan, the MDBA has shown itself to be unwilling or incapable of acting lawfully," the report found.

"That state of affairs exists today, and is the principal reason why there are serious doubts whether the current senior management, and board, of the MDBA are capable of fulfilling their statutory obligations and functions."

Commissioner Walker said the MDBA failed to act on "the best available science" when it was determining how much water could be returned to the environment in the first place.

When explaining the process for approving business cases for water infrastructure projects, designed to help return more water to the river, he also accused the MDBA of being secretive.

"The reasons given for this secrecy have no substance," he said.

"The business cases involve the functions of government, not private enterprise. There is no aspect of commercial-in-confidence — whatever that term is intended to mean — about them.

"Not only is this attitude towards disclosure condescending, it neatly encapsulates the habit of the MDBA, amongst other government entities, to keep matters that should properly be disclosed to the public, secret."

A map of the Murray-Darling Basin in Australia. ( ABC News: Ben Spraggon )

Report finds politics, not science, was driving plan

Commissioner Walker accused the original architects of the multi-billion-dollar plan of being influenced by politics, with the report finding "politics rather than science" drove the setting of the "Sustainable Diversion Limit (SDL) and the recovery figure of 2,750 GL".

"The [water] recovery amount had to start with a 'two'," he said.

"This was not a scientific determination, but one made by senior management and the board of the MDBA.

"It is an unlawful approach. It is maladministration.

"Science, as that term should be understood, was not used. The MDBA has failed to disclose key matters, such as its modelling.

Recently thousands of fish have died in the Darling River at Menindee. ( Facebook: Debbie Newitt )

"Science is open, available, and can be critiqued and checked. It can be validated or invalidated."

The royal commission, which cost more than $5 million, called for new water limits to be set on "the basis of a proper construction of the Water Act, rather than using a triple bottom line approach" and include flood plains.

The "triple bottom line" refers to the balance of social, economic and environmental impacts and was a key consideration used in the Northern Basin Review and SDL, but one which the royal commission highly criticised.

The recent fish kills in western New South Wales were not addressed in the royal commission after the South Australian Government refused the commission's request to look at the issue.

On Thursday, the MDBA said it was confident the basin plan was "made lawfully and based on the best available science".

In a statement it rejected "any assertion by the commission that it has acted improperly or unlawfully in any way".

"Governments are halfway through the implementation of the basin plan," it said.

"More than 2,000 GL of water has been returned to the system, state water resource plans are due to be accredited by the Commonwealth this year, and basin states are developing measures to improve the protection of environmental flows.

"It is vital that this work continues and that the basin plan is implemented in full.

"This is a once in a generation reform that corrects 100 years of overuse, and will take a generation to achieve."

MDBA chief executive Phillip Glyde said it had been a hard-fought battle to establish the independent authority and sign up state and federal governments of all political persuasions to the plan.

"This is the plan, it's very hard to believe that we'd get a better plan agreed by all of those jurisdictions if we were to stop implementation now," he said.

"It's critically important that we continue on."

An aerial view of the Murray River in South Australia. ( ABC News: Carl Saville )

Impact of water buybacks 'greatly overstated'

The royal commission recommended repealing the outcome of the controversial Northern Basin Review, which reduced the amount of water to be taken out of the northern basin by 70 GL.

It wants new determinations of the amount of water from the system that can be used, suggesting more water be reallocated from farm irrigation and returned to the environment.

Commissioner Walker rejected claims from many river communities that buybacks decimate economies of rural towns.

"It is accepted that such a relationship could be debunked by an economics undergraduate," he said.

"There are many other more pertinent, contributing factors to decreases in population or jobs or farm revenue — these include technological change and mechanisation, amongst a number of other relevant factors."

He said the "asserted negative impacts" of water buybacks either did not exist or had been "greatly overstated".

SA Premier says Murray River is the 'beating heart' of the state

The South Australian Government released the report on Thursday after it was handed to Governor Hieu Van Le on Tuesday.

Governor Hieu Van Le received the report from Bret Walker (right) at Government House. ( Supplied: Murray-Darling Basin Royal Commission )

South Australian Premier Steven Marshall described the report as "complex" and said that he would ask Prime Minister Scott Morrison to convene a meeting with the ACT's Chief Minister and premiers of the basin states.

He said the Murray River was the "beating heart of South Australia".

"We are at the end of the river, so it's very important that we make sure that we get every single drop of water that we're entitled to under the plan," Mr Marshall said.

He said 3,200 GL of water must be delivered to the state and that the State Government would consider the royal commission's report and respond in coming months.

"I am not going to respond to the individual recommendations and findings today because I think it is fair enough that we provide a copy of this to every other jurisdiction, we seek input from other cabinet ministers and we will respond accordingly," Mr Marshall said.

He said the report did not focus on the "very serious allegations of water theft" and that the change of the royal commission's focus happened before the Liberal Party was elected in March 2018.

Federal Agriculture and Water Minister David Littleproud said it was "way too early to make an assertions" about whether a separate authority was needed to regulate the plan, but ruled out the need for a national royal commission into the basin.

"This was a royal commission predicated in South Australia. The basin obviously goes further than South Australia," Mr Littleproud said.

"But we respect what the commissioner has done — he's done a significant body of work here that should be respected and looked through.

"We acted in a mature way with leadership, not with politics. You know what? The Australian public have had a gutful of politics. They want outcomes. That's what I'm about."

He said his electorate in Queensland was also impacted by the uncertainty of the Murray-Darling Basin Plan and voters wanted to "get on with their lives".

Mr Littleproud said since he had become Minister for Water Resources "significant improvements" had been made.