The number of waterbirds that call the eastern third of Australia home has dropped to the second lowest level on record, sounding alarm bells for the health of the wider ecosystem as drought conditions take hold. 
The annual aerial survey of waterways and wetlands by the University of New South Wales' Centre for Ecosystem Science found the total wetland area studied was the smallest documented, with 60 per cent of wetlands in the survey area dry. The number of breeding waterbirds was also the lowest recorded.
"Waterbirds are the canary in the coalmine for the ecosystem because they track all of the processes and organisms that are difficult to track at a large scale," said Richard Kingsford, project leader and director of the Centre for Ecosystem Science.
Collectively waterbirds interact with all levels of the ecosystem. Pelicans and cormorants catch fish while herons prefer frogs and smaller fish. Small wading birds such as the sharp-tailed sandpiper opt for further down the foodchain, targeting microscopic invertebrates while swans and coots graze largely on aquatic vegetation.
"They are a great indicator of what is going on in the El Nino and La Nina cycles and what is going on in this drought we are in and the impact of water allocation policies," Professor Kingsford said.
He said areas where water had been allocated, like NSW's Macquarie Marshes and the lower lakes in the Coorong in South Australia, had become a refuge for waterbirds during the dry.
However Professor Kingsford described the results of the 2015 survey as "sobering" because overall it reinforced a trend of long-term decline.
The Menindee Lakes in far west NSW are a stark example. Now dry, they were full four years ago.
2015 was also the first time researchers photographed the Winton Wetlands, near Wangaratta, dry.
Professor Kingsford said the low waterbird numbers recorded in this year's survey was due to drought conditions, which meant birds were dying or failing to breed. However he said breeding rates had been down since 2011-2012, meaning that the existing population wasn't as resilient so any 'bounce back' sparked by improved conditions would take time.  
Conducted in   October-  November for the past 33 years, the post-breeding season survey provides a crucial long-term view of the the health of wetlands and rivers in Queensland, the Northern Territory, NSW, South Australia, the ACT and Victoria.
The findings, which include data on about 50 different species, serve as a reference point for state and federal governments making policy decisions on environmental water flows and guidelines during upcoming duck shooting seasons.
Professor Kingsford said given the results, the duck shooting season in Victoria and South Australia in   March should have serious restrictions.
"When you're down at the bottom of the trough, which is where ducks are, is that if you have a duck shooting season you are really only going to be shooting adults which will reduce the capacity of the population to bounce back," he said.
He said the 2015 waterbird survey highlighted particular species that were in trouble - particularly the Australasian shoveler, glossy ibis and straw-necked ibis.