Experts say the drought will hit irrigated crops like rice and grapes the hardest, because other crops, such as wheat, depend more on rainfall during specific periods.
Corey Watts, of the Australian Conservation Foundation in Melbourne, told the BBC that drought was becoming a regular occurrence instead of happening once every 20 to 25 years.
"We've had a string of reports, official reports, over the last fortnight painting a pretty grim picture for the climate and the future of our economy and our environment," he said. "So now we're looking at a future in the next few decades where drought will occur once every two years."
The Chief Executive of the Murray-Darling Basin Commission, Wendy Craik, said that until there was significant rain and run-off, prospects for irrigation remained grim.
Dr Craik warned that while human demand along the Murray Darling river would still be met, other water requirements might not.
"If the sort of climatic regime we've had in the past couple of years becomes a feature of the future, it's pretty clear we don't have the volume of water available that we've had in the past. Clearly the basin is not going to be the same," she said.
A spokesman for the Bureau of Meteorology National Climate Centre, Neil Plummer, added: "Autumn can only be described as an absolute shocker in terms of climate conditions for the basin".
Government leaders recently agreed an Aus$3.7bn (US$3.6 bn) plan to conserve water in the area.
But scientists say that without sufficient water flow by October, the unique ecology of the lower reaches of the river system will be irreversibly damaged.
Prime Minister Kevin Rudd has already admitted that his government's new conservation plan will not produce results fast enough to meet this deadline.
Large swathes of Australia have been affected by the worst drought in a century, hindering the country's economic growth.
It is estimated that the parched conditions have forced 10,000 farming families off the land in the past five years, and many of those who have decided to stay have introduced more water efficient cropping methods.
This page is best viewed in an up-to-date web browser with style sheets (CSS) enabled. While you will be able to view the content of this page in your current browser, you will not be able to get the full visual experience. Please consider upgrading your browser software or enabling style sheets (CSS) if you are able to do so.