Authorities are concerned up to four people missing across Queensland may have fallen victim to floodwaters.
There are fears the missing people could be added to the two woman who died in flood waters in northern NSW.
Queensland State Disaster Coordinator Deputy Commissioner Stephen Gollschewski said desperate searches were now underway.
"We currently have four people missing about whom we have serious concerns and have deployed significant resources of emergency services to search for those persons," he said.
Communities downstream from Lismore, NSW are at risk from flooding, as raging rivers flow southeast towards the ocean.
Around 20,000 people in the region were ordered to evacuate on Friday after ex-cyclone Debbie dumped heavy rain across large parts of the state's north.
The NSW State Emergency Service rescued 36 people overnight, and deputy acting commissioner Mark Morrow said floodwaters are now heading towards Woodburn and Ballina on the coast.
"We have the Richmond River and Wilson's River coming together today. Cabbage Tree Island has been advised it needs to evacuate and we are working with them as well," he told Channel Nine on Saturday.
Watch: Floodwaters near Murwillumbah
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The Aboriginal community on Cabbage Tree Island was about to be evacuated, Mr Morrow said.
A major flood warning is in place for both the Richmond and Wilsons rivers.
Of the rescues carried out overnight, most involved people stranded on cars and building roofs.
Mr Morrow said many of those rescued were told to evacuate but had decided to stay.
"There's a lesson here for people in the downstream areas that are yet to get this flood," he said.
"Don't do what they did. Make a decision about what you need. Pack early and leave."
Since Wednesday, SES volunteers have rescued more than 400 people and responded to more than 2220 calls for assistance.
Further north of Lismore, residents in Billinudgel, Ocean Shores and New Brighton have also been told to leave.
The Pacific Highway has been cut off by water at Chinderah south of Tweed Heads.
Large parts of Lismore remained under water on Saturday.
Flood warnings are current for the town and its surroundings as well as Chinderah and Murwillumbah, also in northern NSW.
Flood levels in Lismore and Murwillumbah have already broken the records set in 2005 and 2001, respectively.
Watch: Flood effected NSW residents evacuate
The Wilsons River at Lismore peaked at 11.6m on Friday, which was the highest flood peak since 1974.
But there was some good news, with the SES saying "no significant" rainfall had been recorded around Lismore since early on Friday.
Moderate flooding was still occurring along the Richmond River at Woodburn.
However, that could change with the river expected to peak at 4.2m on Saturday and spark a major flood event for the Woodburn community.
In the NSW Hunter Valley, a 64-year-old woman died in a car after it was swept off a causeway at Gungal, west of Muswellbrook, on Friday.
Another woman was found dead by a family member on Friday after she disappeared in floodwaters at the rural property at Upper Burringbar, 20km south of Murwillumbah.
About 220 people spent Friday night sleeping at Lismore Southern Cross University campus' evacuation centre.
While the water is receding in Lismore, it could be days before residents are able to access the damage.
Murwillumbah has suffered significant damage and the repair bill is expected to run into the millions.
Tweed Shire Council general manager Troy Green said water mains had been destroyed, along with waste-treatment plants.
Ballina, Byron, Kyogle, Lismore, Richmond Valley and Tweed local government areas have been declared natural disaster zones.
More floods expected for Queensland
As the clean-up begins in one part of Logan, other parts of the southeast Queensland city are bracing for a fresh wave of flooding.
The Logan River is expected to peak at about 10.5 metres at Waterford West around 2pm on Saturday, in what mayor Luke Smith says will be the biggest flood in the area in more than 40 years.
"That's higher than we saw in 2013 and 2011 and it's getting very very close to that 1974 mark," he told ABC Radio.
Elsewhere in the city the clean-up operation is underway, following record flooding in the Albert River at Beenleigh on Friday.
"We've got two situations going on in the city, where in one area we're looking to see what we need to do and what the damage is and in the second area we're still waiting for the Logan river to peak at Waterford," he said.
He said 323 properties, including 211 houses, are expected to have been inundated by the two floods and residents in low-lying areas have been told to move to higher ground.
Premier Annastacia Palaszczuk on Friday said the height of floodwaters at Beenleigh, where the local train station was swamped, were unlike anything seen before.
The central Queensland city of Rockhampton has been told to prepare for what could be its biggest flood in more than 60 years.
Watch: Flood waters increasing in Chinderah
The weather bureau has warned the Fitzroy River could reach 9.4 metres at Rockhampton on Wednesday, which would equal the level of the city's 1954 floods.
It is expected homes in the Depot Hill area and low-lying parts of Berserker, Allenstown and Kawana will be inundated when the Fitzroy reaches the major flood level of 8.5 metres tomorrow afternoon.
Flooding is also troubling parts of southeast Queensland where more than 300 properties were at risk of being swamped by "unprecedented" floodwaters.
The area's much-loved Yatala Pie Shop fell victim to rising waters, while the new $15 million John Muntz Bridge was ripped apart by the raging Coomera River.
The Brisbane metropolitan area of Logan is expected to be among the worst affected.
Ms Palaszczuk will travel to north Queensland to see the destruction wrought by Cyclone Debbie, after wild weather caused widespread damage across the state.
Despite the focus turning to southeast Queensland and northern NSW following the tropical cyclone, Ms Palaszczuk insists isolated north Queensland communities had not been forgotten.
The restoration of electricity is of particular concern, with 50,000 properties in the Bowen, Mackay and Whitsunday regions still without electricity days after Debbie crossed the coast.
Prime Minister Malcolm Turnbull is urging flood-affected residents to be careful following the two deaths.
"This is a very dangerous time in these flooded areas," he told reporters in Melbourne on Saturday.
"The flooding that has followed is of a very, very dangerous scale in parts of southern Queensland, right through Queensland, and indeed in northern NSW."
While tropical cyclone Debbie has been downgraded, the risk of flooding remains.
"We've had two fatalities, two women in NSW have died as a result of these floods and our thoughts and prayers are with their families.
"This is going to be a tough time for them, but the important thing is everyone should stay safe."
Mr Turnbull has urged residents to listen to the advice of authorities and emergency services.
"I want to say, everybody who is affected by these floods, do not go into these waters," the prime minister said, adding that the waters are expected to rise."If it's flooded, forget it."
