Tropical Cyclone Zelia brought heavy rain and damaging winds after crossing the coast near Port Hedland as a category four on Friday, before weakening to a tropical low as it tracks south.
Efforts to assess damage have been hampered by flooding, with warnings current for the De Grey River and Sandy Desert catchments.
No further flooding is expected in the Fortescue, Ashburton and Gascoyne River catchments, the Bureau of Meteorology said on Sunday.
There has also been no deaths or injuries reported as alert communities escaped the worst of the severe weather, the state government and emergency agencies confirmed.
WA Premier Roger Cook said response teams will move to the Carlindi and De Grey stations after the small communities received "extensive damage".
"We'll be making sure that we can assist those stations as as quickly as possible," he told reporters on Sunday.
"We just have to get in on the ground. It's highly impacted by flood waters at the moment."
A major flood peak was observed at the De Grey River, east of Port Hedland, early on Sunday morning. The river level was falling slowly, but renewed rises are possible as floodwaters arrive from upstream.
Major flooding was also recorded along the Nullagine.
Further rainfall and storms over flood watch areas is possible in the coming days but it is not expected to cause significant flooding, the bureau said.
Emergency crews in WA are assessing the damage, but the downgraded weather system is still dumping significant rain on parts of the Pilbara region, exacerbating flooding.
Major roads have flooded, cutting off critical connections for supply deliveries including the Northwest Coastal Highway between Port Hedland and Broome.
Mr Cook said there is no indication yet when the major highways will reopen.
WA Fire and Emergency Services Commissioner Darren Klemm on Sunday warned heavy rain and flooding was not expected to subside until next week.
Warnings are also in place in flood-devastated areas of Queensland as residents return home to count the cost of the big clean-up.
A flood watch for parts of the Western Cape York Peninsula and a major flood warning for the Lower Flinders River were current on Sunday.
A severe heatwave warning was also issued by the bureau for the North Tropical Coast and Tablelands and Herbert and Lower Burdekin Districts.
Queensland Premier David Crisafulli said efforts have now shifted from response to recovery as residents face a lengthy rebuild.
"The heartache, the devastation, the level of damage is something the likes of which I never thought I'd see in that part of the world," he told reporters on Sunday.
"There are people there who have been cut off from being able to have any form of interaction and resupply for nearly two weeks ... they were pretty happy to be at the local pub in Halifax, I can tell you."
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