There are new claims that the Murray Darling scheme has become a colossal waste of money.

The water infrastructure scheme is intended to change the face of Australian agriculture, but an explosion in very thirsty, high-value crops like nuts could be destabilising the scheme.

It comes after serious questions were raised about Federal Government MPs' involvement in the scheme. 

Reports say over $4 billion in Commonwealth funds has been paid to irrigators to expand their operations and use more water.

It is a big chunk of the $5.6 billion water infrastructure scheme — part of the $13 billion Murray-Darling Basin Plan.

The beneficiaries of the scheme include partly foreign-owned corporations that are transforming vast tracts of land along the threatened river system, planting thirsty cotton and nut fields.

Webster Limited, for example, is a publicly traded company (19.5 per cent owned by Canadian pension fund PSP) responsible for 90 per cent of Australia's walnuts.

Webster has received $41 million from the water infrastructure scheme to hundreds of square kilometres of land in the Murrumbidgee Valley, in south-west New South Wales.

The company is using the money to build dams to store more than 30 billion extra litres of water and irrigate an extra 81 square kilometres of land.

Nut trees require water throughout every year, unlike crops such as cotton, which can be planted according to the amount of water available to sustain them.

Former director at the Murray-Darling Basin Authority, Maryanne Slattery, says the environmental scheme should not be used to give irrigators more water.

“That program was supposed to reduce the amount of water that was going to irrigation, when it's actually increased the opportunities for irrigation … all subsidised by taxpayers,” she said.

“I think Australian taxpayers will be really shocked to find out that that money is actually going to foreign investors as well.”

Ms Slattery says taxpayers are being ripped off.

“There's no government checking in that process at all. There is no confidence that that process has been done independently and is able to be verified,” she said.

“Governments are very motivated to get the savings on paper, and they've got deep pockets … you'd have to expect that some of the savings aren't real, and that money has gone to projects that haven't yielded what they were supposed to.”

UNESCO chair in water economics Professor Quentin Grafton says he has faced brick walls in his efforts to measure the impacts of the scheme.

“It's been incredible to say this, that we can spend [$4 billion] to date yet we haven't done those basic measurements to allow us to know what in fact we've got, net, in terms of the impact for the environment,” he told the ABC.

“In the best case scenario it's less than half of what the Government claims, and in the worst case scenario we've gone backwards, not forwards; that in fact the amount of water in the environment has actually declined as a result of these efficiency subsidies.

“We don't know because we need a water audit, a hydrological audit of what's going on in the basin.”