Up to 120mm of rain is expected to fall in parts of New South Wales, while north Queenslanders are in for a sweaty rest of the week as heatwave conditions set in.
The weather warnings come as Cyclone Uesi barrels through the Tasman Sea towards Lord Howe Island off Australia's east coast, bringing with it larges swells, high winds and more rain.
What's most concerning is the dangerous surf conditions Uesi may cause, with forecasters warning of two-to-three metre swells in Queensland beaches.
It's expected the tropical cyclone will move down the east coast before reaching waters off Sydney on Saturday.
In the meantime, the NSW city of Grafton is forecast to receive as much as 120mm of rain, Sydney, with falls of up to 60mm in some parts of Sydney and 40mm in others.
Weather records could be smashed with a fierce heatwave to expected to hit North Queensland.
Many flood warnings remain in place for much of Queensland, with an alert issued for a woman who disappeared near flooded waterways on the Gold Coast.
⚠️WARNING UPDATE: The immediate threat of heavy rainfall in #SEQld has passed. As always, we will continue to keep a close eye on any storms that develop, and further warnings will be issued if required. Note numerous flood warnings are current: https://t.co/zV4t3F2GeX pic.twitter.com/xkCLS7Urkk— Bureau of Meteorology, Queensland (@BOM_Qld) February 12, 2020
Police say 26-year-old Yang Chen was reported missing about 11am on Wednesday by a man who said he was walking near Gorge Falls in the Tallebudgera Valley when he lost sight of her.
Authorities warn a number of creeks in the area have been affected by recent rainfall and there are concerns for Ms Chen's safety.
Meanwhile, the rain has impacted hundreds of residents on Queensland's Sunshine Coast who were left to deal with power outages and submerged roads when the region was hit by torrential rain and flash flooding.
A severe thunderstorm warning for the region and parts of Gympie and the Moreton Bay Council area was issued late on Wednesday, while Cyclone Uesi is creating large swells along Australia's east coast.
The cyclone is expected to pummel beaches south of Fraser Island, with the Gold Coast expecting the heaviest surf on Thursday.
The Bureau of Meteorology warned of possible intense rainfall leading to life-threatening flash flooding, noting 79mm of rain was recorded at Yandina Creek in just one hour on Wednesday night.
Sunshine Coast Airport copped 140mm of rain in three hours and Coolum was hit with 125mm over the same period.
Almost 2000 customers were affected by power outages on the Sunshine Coast, Energex reported shortly before 1am on Thursday.
The Department of Transport and Main Roads reported roads were flooded at various locations including Doonan, Sippy Downs, Mount Coolum, Tewantin and Nambour.
Inland, properties remain under threat in tiny communities isolated by an inland sea of floodwater west of Brisbane, in the state's far north locals are bracing for searing heatwave conditions.
Residents in Jandowae on the Darling Downs watched the water rise quickly after storms dumped 100mm of rain on Tuesday night onto an already-soaked catchment.
"We are on the creek and can report biggest flooding I can remember," Lee Labrie posted on social media.
"Probably the worst flooding in a long time," Rob Norman wrote.
Rising waters in the Jandowae Creek and across the Jimbour Plain were expected to cause further flooding in the region on Wednesday night.
An emergency flood alert was issued for Warra, 25 minutes from Jandowae, with residents advised to secure their belongings, prepare to leave and warn neighbours.
Other parts of Queensland remain on flood watch, with warnings for coastal catchments between Bundaberg and the NSW border.
However, it is a very different story in the state's far north where residents are bracing for heatwave conditions into the mid-40s with February temperature records expected to tumble.