Climate change is combining with Australia's record-breaking drought to strangle the nation's largest river system, threatening to devastate food supplies, a report said Wednesday.

The government's Murray Darling Basin Authority said water flow was near historic lows in the system, which provides water to Australia's "food bowl", a vast expanse of land almost twice as big as France that runs down the continent's east coast.

Water storages were at just 16 percent of capacity, and at less than one-third of the January average, with a recent once-in-a-century heatwave slowing some areas to a trickle.

"There's no doubt we've got this alignment of long-term change, climate change, and we've got the short cycle, this incredible drought,' said Rob Freeman, the authority's chief.

"They've combined in the most wicked way."

Hundreds of fish had died in the mid-Murray due to the elevated temperatures, and there was a high risk of a toxic algae outbreak, said Freeman.

The Bureau of Meteorology said climate change would drive temperatures up by between two and four degrees Celsius (36 and 39 degrees Fahrenheit) in Australia over the next 100 years.

"We've seen large increases in heatwaves globally over the last hundred years. That's going to continue. It's going to accelerate," said the National Climate Centre's David Jones.

"Those kind of temperatures that only happened once every two or three decades, we're now seeing almost on an annual basis," Jones told the Australian Broadcasting Corporation.

Australia is in the grip of the worst drought in a century, which has stretched for more than seven years in some areas and has forced restrictions on water usage in the country's major cities.

A government-commissioned report on climate change last year warned that exceptionally hot years, which used to occur once every 22 years, would occur every one or two years, virtually making drought a permanent part of the Australian environment.