Billions of dollars have been wasted along the Murray-Darling Basin on irrigation projects that have failed to achieve their intended environmental outcomes, a group of 12 concerned Australian academics says.

The group, which includes economists and some of the nation's top water scientists, released a declaration in Adelaide this morning urging fundamental changes to the way the system is administered.

Those changes include halting subsidies and grants to irrigators that have been introduced under the Murray-Darling Basin Plan.

According to the researchers, $6 billion has already been spent on water recovery projects across the Basin, including $4 billion to subsidise irrigation.

"For many of these projects there is no scientific evidence that they have actually increased net stream flows," the scientists stated.

"Despite allocating half a billion dollars in 2007 to upgrade water meters in the Basin, as much as 75 per cent of all surface water diversions in the northern part of the Basin may still not have water meters."

The criticisms have been rejected by the Federal Government, the Murray-Darling Basin Authority and the National Irrigators Council.

The declaration also calls for an independent audit of all water recovery measures across the Basin, and a new scientific body to advise governments on the implementation of the 2007 Federal Water Act.

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

Former head of CSIRO Land & Water, Professor John Williams, said the science underpinning current water policy was deeply flawed, and called for immediate changes to ensure more water flow through the system.

"We've got to have a river system that has sufficient water flow to flood, recharge ground water, take salt to the ocean and provide wetlands and habitat," he said.

"Our current system is not doing that."

According to data cited by the scientists for The Conversation, buying water back from irrigators is "60 per cent cheaper" than spending on irrigation engineering projects.

Professor Williams said currently, authorities were "playing accounting games" that made it "look as though we're doing something".

Eight of the 12 economists and scientists who have signed the declaration. ( ABC News: Sarah Hancock )

Both Professor Williams and Associate Professor David Paton from the University of Adelaide described the Coorong in South Australia as a "barometer" for the system's health.

Professor Paton said the number of migratory birds in the region has declined hugely since the 1980s.

"The last two years have probably been the two lowest abundances... that we've had in the system ever, lower than they were during the Millennium Drought," he said.

"The Murray-Darling Basin Authority simply says 'we're not expecting recovery until the plan's been delivered, until 2024'. Well sorry, you've been putting water back. You should start to see some recovery if it's really going to make a difference."

Professor Paton said a plan to transfer water into the Coorong was misguided and would permanently alter the nature of the area.

He also said the nation was not meeting several of its international environmental obligations, including the Ramsar Convention, and accused the Federal Government of indifference.

"The Prime Minister said we're a country that abides by our international obligations. This is an international obligation that all governments are just turning their backs on," he said.

'Simply not true': MDBA rejects declaration

The MDBA said the Basin Plan was a "visionary, long-term policy". ( Supplied: Matthew Chapple )

The agency tasked with overseeing the multi-billion-dollar basin reform plan, the Murray-Darling Basin Authority, has hit back at the scientists' claims.

"Claims that the plan's investment in more modern and efficient water infrastructure is not delivering benefits for the environment are simply not true," chief executive Phillip Glyde said.

The authority said the plan was a "visionary, long-term policy" and that water infrastructure efficiency programs had already helped recover water for the environment.

"The Basin Plan was neither expected nor intended to deliver immediate results," Mr Glyde said.

"It is simply not possible to repair 100 years of damage to such a vast river system overnight, or even within five years."

Federal Assistant Water Minister Anne Ruston said the recommendations did not factor in the economic needs of farming communities in the basin, and that favouring water buybacks could be harmful.

"We can't just decimate out regional communities by buying back water out of them and leaving them with no means of future existence," she said.

"The report is strong on motherhood statements but light on science and fact … and also fails to recognise the implantation of the plan is a 12-year process.

"The first people to be screaming at us for not delivering the plan on time will be these people [the scientists], and yet they are now the ones telling us to stop the plan."

National Irrigators Council CEO Steve Whan also criticised the scientists' findings, saying the benefits would be witnessed by future generations.

"The important thing about this to remember we are five years into a plan that is going to take a number of years to implement, but [it takes] decades to see good environmental outcomes," he said.