Scientists believe Murray-Darling bird numbers have more than halved in the last 30 years.

Researchers conducting an annual aerial waterbird survey have just completed their most comprehensive analysis ever of the river system.

University of New South Wales Professor Richard Kingsford is now into his 32nd year of surveying.

"We've been doing these surveys since 1983 and we've seen a 60 per cent decline in waterbird numbers since then," Professor Kingsford said.

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"Largely that's due to the impacts of building dams and developing our wetland systems and taking water out of rivers so these places don't last as long."

Sorry, this video has expired Professor Richard Kingsford speaks to Jake Sturmer

Professor Kingsford said waterbirds were a key indicator of the health of the system.

"You can see what's happening to water quality, you can see what's happening to fish populations, and so they're a very good barometer of what's going on in our river systems," he said.

His survey finished at Lake Cowal in central New South Wales, where many species of waterbirds had congregated this year.

"Lake Cowal is a wonderful oasis," he said.

"There's nowhere else in the Murray-Darling at the moment like this – there are tens of thousands of waterbirds."

Murray-Darling last drought-safe haven for waterbirds

The Murray-Darling is rapidly becoming the last resort for waterbirds.

Professor Richard Kingsford says as surrounding lakes have dried up, Lake Cowal may not last much longer. ( ABC News: Jake Sturmer )

"The thing that's really struck me about this year is normally we will find quite a few lakes that even in the big droughts, even in the millennium drought, sort of 2006-2009, there were a few big lakes hanging on," Professor Kingsford said.

"It's a real big worry that this particular year we're not seeing any of those lakes.

"This is a very important lake, Lake Cowal, but it's not going to last much longer."

It means many of the tens of thousands of the birds currently in Lake Cowal may die.

Terry Korn, a former executive director at the NSW National Parks and Wildlife Service, believes the survey provides crucial data to measure river health.

"This survey provides good baseline data over a long period for planning for water management within the Murray-Darling Basin," he said.

"Without that long-term data we're really behind the eight ball in determining how the basin plan will affect changes throughout the basin."

Space to play or pause, M to mute, left and right arrows to seek, up and down arrows for volume. Listen Duration: 3 minutes 12 seconds 3 m 12 s Decline in Murray-Darling waterbirds a bad sign for river system ( Jake Sturmer ) Download 5.9 MB

He believes the abolition of the National Water Commission by the Abbott Government is a mistake.

The Commission provided national direction for the management of water.

"I think it's critical we still have that, especially in this eastern part of Australia where irrigation industries are highly developed and we need to get that balance right between irrigation and the environment," Mr Korn said.