New research has found a dramatic decline in water birds in the Murray-Darling Basin, with numbers down about 70 per cent in the past three decades.

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A University of New South Wales team found the alarming drop after crunching 32 years of data.

The study has been published today in the Global Change Biology journal.

Director of the UNSW Centre for Ecosystem Science, Richard Kingsford, who surveys up to 2,000 wetlands around Australia annually, headed up the research.

"We survey all water bids from pelicans to swans to sharp tail sandpipers — which are migratory shore birds — egrets and ibis," he said.

"We found that more than 70 per cent decline in water bird numbers, and there is a big issue here as we compared one river basin with no dams and the other with dams — the Murray-Darling Basin — and most of that decline was in the Murray-Darling Basin wetlands."

The Murray-Darling Basin has 240 dams and stores 30,000 gigalitres of water. The similarly sized Lake Eyre in South Australia has only one dam.

The scientists found between 1983 and 2014 there were no significant changes in water bird numbers in the Lake Eyre Basin.

Their analysis of the Murray-Darling however found an alarming reduction in dozens of water bird species.

A map of the Murray-Darling Basin in Australia. ( ABC News: Ben Spraggon )

"The birds have either died or they haven't bred as much as they did in the past, what we expected in the past," Professor Kingsford said.

"We separated that group into all of the birds that eat fish, all of the birds that eat invertebrates and vegetation, and what we're seeing is that all of those groups are also declining, which tells you the whole of the ecosystem is in decline."

Basin's birds can bounce back

The scientists concluded there was a strong link between river flows and the number of birds.

And it is not all bad news for the basin, with the research showing the birds could bounce back.

Professor Richard Kingsford has been counting birds continuously for 32 years. ( ABC News: Ann Jones )

"What we found was when we looked at the models and put back the water coming back into the basin as a result of the environmental flows and the buy-back of water, that over the decades [it] would actually bring back the original population by 20 per cent of where it was," Professor Kingsford said.

He added the Lake Eyre basin was in good shape.

"The really good news is that the other basin that we looked at, the Lake Eyre basin, is one of the most pristine and wonderful river basins in the world, and whatever way we look at that it's travelling pretty well," Professor Kingsford said.

"We can't see any sort of changes in any sorts of waterbirds."

Ecologist Terry Hillman, who has been studying the Murray-Darling system since the early 1970s and advises the Murray-Darling Basin Authority, said the study provided valuable information.

"It demonstrates pretty clearly that we can manage these rivers for all sorts of human activity whether the cost is worth it or not," he said.

"A lot of these arguments are done on the basis of prejudice, and sometimes political prejudice, and to have factual information there to work on makes a great deal of difference, or it should do anyway.

"At a time when there is a lot of pressure to sure up the supply of water to irrigation, there is now a better indication on what the cost of doing that is and it's up to the community to decide whether they want to pay that cost or not."

A Murray-Darling Basin Authority spokesperson said the organisation was keen to collaborate with the research community.

"Over the coming years we will continue to work with governments, local communities, and researchers to work toward a healthy and productive basin," they said.

"This year, the MDBA is releasing multi-year environmental priorities that identify specific sites, ecological communities, and species including birds that require support over the next three to five years."