Although the basin's manager, the Murray Darling Basin Authority (MDBA), welcomed the Wentworth Group of Concerned Scientists' study, it doesn't not believe the report tells the whole story.

The report by eminent river scientists measured how much water actually flowed past 27 river gauges across the Basin compared to how much was expected to flow at these gauges, under Basin Plan modelling, since 2012.

After accounting for drought and the variable amounts of water available in each year, the valley-by-valley assessment found more than 1200 billion litres failed to reach the South Australian border every year, while Wilcannia on the Darling River received 230 billion litres less than expected every year.

"24 of 27 river sites across the Basin received less water than expected at this stage of Basin Plan implementation, even accounting for the drought conditions, and three sites received less than half of what was expected," researcher Professor Fran Sheldon said.

The Wentworth Group propose several reasons for why the water was missing, including climate change, water theft, floodplains being interrupted and on-farm efficient measures reducing the amount of water returning to the system.

The report also suggests the MDBA's original modelling may have been flawed, exaggerating the amount of water available.

Regardless of what combination of reasons are responsible, the scientists say there needs to be greater transparency in water management, and called on governments to publish flow measurements across the basin to ensure rivers and communities are benefiting as expected.

"Governments must do a much better job of reporting outcomes from the $13 billion being spent on water reforms," researcher Professor Jamie Pittock said.

MDBA executive director Vicki Woodburn said the study was a "valuable contribution" to the scientific understanding of the basin, however the MDBA's analysis - which measures much more than just flows - showed the plan was improving the environment.

"Our analysis also shows that the recent drought - that saw record high temperatures and low rainfall - meant that flows in the river system were inhibited," Ms Woodburn said.

"In addition to hydrology, we also draw on data and expert advice for other aspects of the system. Our analysis illustrates that in the past seven years, the Basin Plan has increased flows and is making a difference to the environment."

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Ms Woodburn said it was important to measure more than just flows, which were not targets within the basin plan.

"We work with our state and federal colleagues to also measure bird and fish breeding, vegetation health and the health of complex ecosystems like the Gwydir wetlands and the Lower Lakes," she said.

"We invest significant resources to check if the environment is responding to managed environmental water - and we know it is."

By the end of the year, the MDBA will release its own analysis of how the plan is going, which will draw on hydrological analysis and evidence from environmental scientists, the state agencies and river operators.