The Murray-Darling will likely end up worse off under the Basin Plan, a senior Murray-Darling Basin Authority whistleblower has warned.

David Bell, an experienced water planning expert, worked at the Murray-Darling Basin Authority (MDBA) from March 2009 until his retirement as director on November last year.

In a statement to the Murray-Darling Basin Royal Commission, Mr Bell paints a picture of the planning and implementation of the Basin Plan that was heavily influenced by the need to strike an agreement with "hostile states", vested interests and flawed science.

He said the formation and the implementation of the plan had come under significant pressure to "water down" environmental targets to appease upstream states.

"Following implementation of the basin plan, I consider there has been some unnecessary undermining of it, including through failure to recover real water; buying water back at inflated prices and acquiring water back through efficiency measures," Mr Bell said in his statement.

"I think some of that water is fictitious, which undermines the water rights system.

"The numbers don't mean very much anymore and that is very worrying."

The dry bed of Lake Menindee overgrown with vegetation in April. ( ABC News: Declan Gooch )

Plan to shrink Menindee Lakes 'environmental vandalism'

At worst, the sustainable diversion limits (SDL), or the amount of water able to be used in the basin, could soon be meaningless or effectively allow people to take more than before the federal Water Act 2007 came into effect, he said.

"In my view some SDL projects create a risk of serious harm to the environment," he said.

"In that regard, the proposed Menindee Lakes project is nothing short of environmental vandalism and should not proceed.

"It will have very serious impacts on the wetland system and serious impacts on golden perch."

The controversial project to reduce the size of the Menindee Lakes risked making golden perch extinct, he said.

Water use figures 'hastily' arrived at

Mr Bell said early in his employment at the MDBA, he was given the job of hastily coming up with an estimate of the SDL within half an hour.

"From memory, I came up with a recovery number in the vicinity of 4,000 to 4,500 gigalitres," he said.

Ultimately, 2,750GL was settled upon as a "compromise" to meet the needs of "hostile" states and vested interests, he said.

He said "there was no suggestion this deal was based on the best available science", with watering down of the plan occurring since it was finalised in 2013.

Authority not independent

Mr Bell used his statement to the royal commission to accuse the MDBA of not being independent of government and failing good governance as the creator, implementer and judge of the success of the Basin Plan.

The board members are vetted by the Government and the states have a say and the Agriculture and Water Resources Department exercise influence over the MDBA's activities, he said.

"From my perspective, the authority would be established by a new board and senior management," he said.

"From a legislative perspective, I consider that the authority would be better served if it was set up under its own act."

Mr Bell will give evidence to the royal commission's public hearings, starting in Adelaide on Monday.