People in Fitzroy Crossing and surrounding communities have been urged to relocate, with an evacuation centre established at the local recreation centre.
Major flooding is also expected to impact Willare, Noonkanbah, Mount Barnett and Christmas Creek on Tuesday and Wednesday.
The Bureau of Meteorology says the weather system is centred just north of Halls Creek and is expected to move slowly west over the next 24 to 36 hours and will be just east of Broome on Tuesday evening.
A vigorous monsoon flow wraps into the system which has dumped between 200 mm and 500 mm of rain since Saturday.
"Further widespread heavy falls are forecast for the next few days," the bureau said on Tuesday.
"River rises and areas of flooding are adversely affecting road conditions in the Fitzroy River catchment. Some roads may become impassable and some communities are now isolated."
Emergency WA said there was a possible threat to lives and homes due to rising rivers and streams with the water fast flowing and levels rising quickly.
Meanwhile, flood levels are holding steady at a western NSW town.
A flood peak of up to 10.7 metres had been tipped to hit Menindee on Monday, above the 1976 record of 10.46 metres.
But the bureau has since revised its forecast, declaring further rises to 10.7m are possible from and around Thursday.
Locals from 31 properties around Menindee were advised to evacuate before New Year's Eve, with residents from seven or eight heeding the warning.
Elevated river levels are expected to remain around the 10-metre mark for at least another fortnight as water continues to flow through the Darling River, the bureau said.
In other parts of the country, heatwave conditions have persisted over the past few days, with the worst of those in central WA, western Queensland and northeast South Australia.
Also in SA, the continued surge of water down the Murray has breached or inundated a string of agricultural levees including those at Mypolonga, Toora, Mobilong, Cowirra, Wall Flat, Long Island and Long Flat.
The State Emergency Service said more issues with levees could be expected as peak flows moved down the river.
The Murray is expected to peak at Waikerie and Morgan between now and January 7 and at Blanchetown, Swan Reach and Mannum between January 4 and 13.
In the Northern Territory, a severe weather warning for the Daly, Tiwi and Arnhem districts has been cancelled as damaging surf conditions ease.
A vigorous monsoon flow is continuing across the western Top End, but coastal wave heights are abating.
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