Downpours have already occurred in parts of South Australia's thinly populated north, cutting many roads and the East West rail line that links Adelaide to Perth.
Wet weather with significant accumulated rainfall totals was expected to continue across the area in the coming days, SA's State Emergency Service warned.
River and creek levels are rising, triggering localised flooding and overland inundation that could continue with additional rainfall.
The Australian Rail Track Corporation said the East West corridor remained closed on Monday, with sections of the track washed away between McLeay and Bookaloo in SA.
It could not confirm when services would resume but said with further flooding expected, restoration work could take more than a week.
Lines between Port Augusta and Whyalla, and Port Augusta and Broken Hill in NSW have reopened.
"I understand that crews are being dispatched to get on top of ... how they're going to go about reopening it up as quickly as possible," SA Premier Peter Malinauskas told reporters.
"It's not just a passenger line. It's also just as critical as a freight route."Â
A severe weather warning has been issued for the Northern Territory, outback Queensland and South Australia due to an intense low-pressure system over the NT's southeast.
Major rainfalls have cut roads in the NT, with Alice Springs residents again bracing for flash flooding.
A downpour earlier in February inundated the usually dry Todd River, triggering multiple rescues in Alice Springs including a woman who clung to a tree for 11 hours.
In Queensland's northwest, floodwaters have cut roads, triggering multiple rescues and panic buying with supermarket shelves in Mount Isa stripped bare.
Mayor Peta MacRae urged locals to be patient amid supply chain issues.
"The highway opened for about 10 hours on Saturday, so my understanding is that shelves were refilled today," she told AAP.
"The groceries will come through, and there's contingencies in place if the trucks can't get through."
Nearby Gulf Country between Normanton and Julia Creek was devastated by flooding in January, with stock losses of more than 100,000 reported.
For grazier Peter Ashman, who runs Escombe Downs station near Winton, the news has been good this season.
"This is a good story for us a bit further west and up near Mt Isa," he told AAP.
"With this amount of rain and this amount of feed, we'll go right through April, May, June next year. It'll see us through."
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