A former CSIRO scientist has accused the Murray-Darling Basin Authority (MDBA) of "interfering" in his research, around the time environmental goals were being developed for the Basin Plan.

Australian National University lecturer Dr Matthew Colloff led a team of researchers in 2010 and 2011, as part of a project called the Multiple Benefits report.

The project was funded by the Murray-Darling Basin Authority.

Dr Colloff's team was asked to determine "the ecological and economic benefits of environmental water in the Murray-Darling Basin".

The retired scientist this week made a submission to South Australia's Royal Commission into the use of Murray-Darling Basin water, offering a scathing account of his experiences with the MDBA.

'Scientific integrity' had been compromised

He said he felt his "scientific integrity" had been compromised during the creation of the Multiple Benefits report.

"I was unhappy with the extent of the MDBA's interference throughout the course of [the project]," he said.

Dr Colloff's submission has also cast doubt on the modelling used by the MDBA. ( ABC Rural: Tom Nancarrow )

"The MBDA attempted to influence CSIRO findings on several occasions.

"For example … in a draft of the Multiple Benefits report … we had included a table and some narrative about our hydrological modelling… which the MDBA requested that we remove.

"It didn't compare favourably with their own modelling."

Dr Colloff said the MDBA "seriously micromanaged" the project, and tried to "direct" the team as to what should and should not be included in the report.

"We were being managed … in such a way that our job became effectively a rubber stamping of the MDBA's findings," he said.

Submission casts doubt over MDBA

Royal Commissioner Bret Walker SC is examining the effectiveness of the Basin Plan, and whether it is being properly implemented by state and federal authorities.

Dr Colloff's submission has also cast doubt on the modelling used by the MDBA, before it nominated 2,750 GL as an appropriate environmental water target for the final Basin Plan.

Dr Colloff said that towards the end of 2010, the MDBA asked his team to model ecological outcomes for "scenarios of 3,200 GL, 2,750 GL and 2,400 GL".

"We refused on the basis that the project had nearly finished … and that there were too little difference between the scenario volumes to be able to show ecological benefits," he said.

"We were concerned that if we found no significant differences between 2,750 and 2,400 GL, then this finding could be used as justification for adoption of the lower volume.

"What was clear to us … [was] that they were constantly iterating down the environmental water requirement."

Other submissions to South Australia's Royal Commission have raised concerns about the MDBA's modelling around the 2,750 GL target.

The Murray-Darling Basin Authority said it had "no comment to add at this time".