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In the end, the modelling centred on 2800 GL, or close to the 2750 GL the authority eventually settled on for its so-called Sustainable Diversion Limit.

The results showed "quite marginal improvements when compared with a 'baseline' scenario," he said.

"It was about suppressing the research they didn't want to see," Dr Colloff said, with only the Coorong at the end of the system showing much benefit.

Even that outcome, though, was in comparison to 2009 at the end of the Millenium Drought when the region was on the brink of becoming "an acid-sulphate swamp", he said.

Dr Colloff, who retired from the CSIRO in 2016, said he raised the issue with CSIRO managers who did not offer support, saying in effect, "if we don't do what we're asked we won't get paid".

The authority declined to comment. Fairfax Media also approached Agriculture Minister David Littleproud and Labor water spokesman Tony Burke.

The CSIRO's research "was guided by a Scientific Reference Panel and overseen by a Project Steering Committee, and outputs reviewed by an Independent Scientific Review Panel made up of representatives from Griffith University, The Centre for International Economics, Edith Cowan University, EcoInsights, and Barma Consulting", a spokesman said.

The Royal Commission resumes hearings on Wednesday. At its first day of hearings last week, Richard Beasley, SC, the counsel assisting Commissioner Bret Walker, described the basin plan as "a fraud on the environment" that may be in breach of the Water Act.