Flash flooding has struck the country's table grape hub of Mildura in Victoria's northwest at the peak of harvest season after 100mm of rain fell in 24 hours.
Fruit growers in the region are fighting to save their vines as more downpours threatened across Australia, with far north Queensland bracing for a potential cyclone.
Mildura is reeling after being inundated by 65.8mm of rain, beating a March daily rainfall record that had stood since 1894.
Growers are frantically pumping out floodwater as they pin their hopes on clear skies and cool temperatures.
It was vital farmers accessed crops to spray fungicides and protect the fruit at risk, local grower Anthony Cirillo told AAP.
"Nowadays, 99 per cent of the growers are covering their fruit for protection which has helped a lot," he said, after his family's Alpha Fresh farm copped 165mm of rain in three days.
"But now we've got to fight against the pressures from the humidity and obviously, the ability to get back into the actual farm because there's no harvesting happening anywhere."
While the clean-up is under way, it will be some time before the damage's full extent will be realised.
The deluge was the last thing local growers needed, Australian Grape and Wine CEO Lee McLean said.
"For many regions like the Murray Valley around Mildura ... this is creating pretty disastrous, diabolical kind of conditions," he told AAP.
While most of the white grapes have been harvested, only 10 per cent of the red crop has been picked.
"There will be fairly significant crop losses and for the grapes that might still be on the vine, the hot, humid, wet weather tends to bring a whole heap of disease pressure," he said.
But the rain has been a boon for Mildura's citrus growers, who are hoping for a bumper crop.
"It's great for the trees, they love it, but not so good for the vines," Mildura Fruit Company's Rohan Ashley said.
"It's no good for the dried vine fruit growers - there is the potential for them to lose all their crop.
"If it stays wet and humid, the fruit will just go rotten. And table grapes, they're probably going to split."
Australian growers produced about 200,000 tonnes of table grapes in 2021/22 across 25,000 acres, with an estimated 70 per cent grown for export.
Flash flooding has affected much of inland Australia in recent days, claiming the life of a motorcyclist who tried to cross an inundated creek at Eurelia, in South Australia's Flinders Ranges, on Sunday morning.
Rising floodwaters also caught out a truck driver at Yunta, SA who was winched to safety by a rescue helicopter on Sunday afternoon.
In the Northern Territory, an emergency situation has been declared for parts of the Barkly and Central Australia regions, with two schools in Alice Springs closed on Monday to be used as shelters.
Queensland's far north is also set to get wet with a tropical low in the Coral Sea now a 25 per cent chance of becoming a cyclone by Thursday, the Bureau of Meteorology says.
The system located east of Willis Island may track into the state's southeast to provide welcome rain or move west inland, joining forces with another low.
That would be bad news for graziers in the Gulf Country, with the Flinders and Cloncurry Rivers already in flood.
Huge falls are forecast for the Wet Tropics this week, with 286mm falling overnight at the Abergowrie Bridge near Ingham and major flooding also declared in the Herbert River.
Large areas of the outback are already underwater, with some remote Queensland communities expected to be isolated for weeks.
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