Police say they believe the deceased are a 26-year-old man and 23-year-old woman - believed to be Chinese nationals - who disappeared while driving from Brisbane to Queensland's flood-ravaged North Burnett region.
The first flood-related deaths in the rain-hit region has devastated the community of Gympie, where the bodies were found, local mayor Glen Hartwig said.
"They are two young people who have sadly passed away," he told AAP.
"For their families who have to deal with this heartache, our thoughts and prayers go out to them."
The disappearance sparked a search of the area from Kilkivan to Mundubbera, west of Gympie, where floodwaters had inundated communities.
Police, SES volunteers and helicopters scoured the region from Wednesday morning, later locating a silver vehicle at Kilkivan Tansey Road.
Police later confirmed two bodies had been found in the car, with divers and forensic teams remaining at the scene to investigate.
The region near where the vehicle was found had been one of the hardest hit by wild weather, Mr Hartwig said.
Up to 400mm of rain fell in 24 hours before floodwaters "absolutely smashed" western areas including Kilkivan, Goomeri, Woolooga, Tansey and Manumbar.
Crops, fences and roads were destroyed but the full extent of the damage won't be known until floodwaters recede.
"There's significant infrastructure damage. It is going to take a long time to repair," Mr Hartwig said.
"Looking at the financial impact on farmers, it will be 12 months before they will take any money from these paddocks that have been destroyed."
The Chinchilla community northwest of Brisbane is next in line after Bundaberg was flooded on Wednesday, inundating hundreds of houses and businesses.
Police issued an emergency declaration at Chinchilla, setting up an exclusion zone in the Western Downs town as floodwaters threatened.
An evacuation area has been established at the Chinchilla showgrounds, with at least 10 businesses inundated.
Chinchilla's flooded Charleys Creek was expected to reach a 6.8-metre peak on Thursday, local mayor Andrew Smith told AAP.Â
Residents are clinging to hope that Charleys Creek, which runs through the town, would not reach the devastating flood levels of 2011.
Back then, Charleys Creek reached a record peak of 7.45m, flooding scores of homes and damaging the prized local watermelon industry.
Door-knocking began in the community's low-lying areas late on Wednesday warning residents to evacuate before a number of people were reportedly rescued from a campground.
Further west, Longreach is bracing amid fears low lying houses may be impacted in the coming days.
In the Northern Territory, multiple flood warnings and watches are in place across the saturated Top End.
The clean-up has begun at Katherine but hundreds remain in emergency shelters after their homes were inundated and some are still without power.
The nearby Katherine River was likely to peak at 17 metres on Thursday night.
Darwin and Palmerston residents have been told to keep boiling water despite nearby dam pumps restarting after they were shut down by flash flooding.
A mother and her children were rescued from a roof when flash flooding hit south of the NT capital on Monday, swamping about 20 homes,
The federal and NT governments on Thursday announced extended assistance to flood-hit communities.
21°C