About 300 billion litres of environmental water has been "lost" in the Murray-Darling Basin in recent years as farmers have been heavily subsidised to improve their irrigation practices, according to a leading water scientist.

John Williams, a foundation member of the Wentworth Group and a former chief of CSIRO Land and Water, said the volume of water loss is 50 to 100 times greater than the allegations of illegal pumping and fraud in the Barwon and Darling Rivers exposed by Four Corners earlier this week.

Dr Williams told RN Breakfast that the problem was occurring across the entire Basin because the Murray-Darling Plan had not addressed the problem of "return flows".

This is the water that used to leak back into the rivers as environmental flows when it was not used on farms by irrigators.

Economist professor Quentin Grafton from the Australian National University (ANU) estimates the Government has spent about $3 billion over the past five years subsidising farmers to capture and use more of this water.

But Dr Williams said: "Unless you take account of the return flows, and adjust your extraction appropriately, you are actually starving the river of what it used to have as environmental flows."

He has calculated the loss to the environment is around 300 gigalitres of water — about three-fifths the volume of water in Sydney Harbour.

'At the moment we're flying blind': Experts want return flow audits

Dr Williams and Professor Grafton from the ANU's Crawford School of Public Policy are calling for a moratorium on $1.7 billion of new water infrastructure spending budgeted over the next four years in the Murray-Darling.

Dr Williams and Professor Grafton also want an audit of return flows from irrigation works back to the environment.

"I think it's very reasonable to say, 'Let's have an audit, let's look at what the numbers tell us in terms of return flows'," Professor Grafton said.

"Then we can decide where we want to spend our money.

"At the moment, we're flying blind, based on trust that this is working.

"We can fix this, but we just have to know the numbers … [with] the subsidies spent on on-farm water use efficiencies we've actually gone backwards … every dollar we spend on that, we actually reduce stream flows and environmental flows."

Dr Williams said there has been little scientific scrutiny of the Government's water efficiency program, despite emerging international concern about the potential environmental losses.

"The Food and Agriculture Organisation and major hydrological papers … have been pointing out [this problem] right around the world.

"That if you use water use efficiency, which sounds attractive, without substantially reducing the take … that you do not go forward.

"That's written in the literature. But in the current Murray-Darling Basin Plan that has not been properly taken into account."

Dr Phillip Glyde, the chief executive of the Murray-Darling Basin Authority, told RN Breakfast "we certainly recognise that Dr Williams is an expert … John's talking about the potential for up to 300 gigalitres of water that might be being lost through return flows".

"There's great debate about that and about that measurement," he said.

"The important thing though, is that with those water use efficiencies the water ends up in the hands of the Commonwealth Environmental Water Holder, and they can choose to use the water in a much more efficient way … choose to mimic natural events to add on to existing flows."

Sorry, this video has expired Who is benefitting from the billions spent on the Murray-Darling?

Murray-Darling Basin Authority CEO says plan is 'on track'

Dr Glyde conceded that half of the return flows that used to return to the rivers are now being kept by irrigators.

Asked if the extraction volumes to irrigators are being correspondingly reduced as water efficiencies are increased, Dr Glyde said: "It is happening … [but] there needs to be more."

Dr Glyde said there was no need for a moratorium or a new audit on return flows, because that work was already being done.

"It is, and each of the environmental water holders — Commonwealth and state — do those regular reports and audits and they report on the outcomes of that work, good and bad," Dr Glyde said.

He said he understood the frustration of ecologist Dr David Paton in South Australia, who claimed on RN Breakfast that the ecological health of the Coorong and Murray mouth is as bad as it has ever been.

pumps going into the Murray-Darling Basin, belonging to Webster Limited. July 21, 2017. ( Four Corners )

"Dr Patton's right in that the Coorong and the lower lakes, the Murray mouth, are really the canary [in the coalmine] — rivers die from the mouth up," he said.

"It's really important to understand though that the Basin Plan currently now is delivering more water than would have been the case beforehand.

"We're five years into trying to restore 100 years of over allocation of the water in the Basin. Any environmentalist will tell you, you will not be able to get immediate results.

"My message would be that we've got to stay the course — there is no plan B.

"The thought of pausing like Dr Grafton's suggesting makes no sense at all to me.

"We're on track and we're going to deliver."