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