The emergency escalated quickly during the day, with more than 30 low-lying suburbs on high alert and inner-city suburbs including West End and Fortitude Valley being evacuated.
As the Brisbane River breached its banks in several place to engulf parks and footbridges and heavy rain continued to fall on the metropolitan area, the city's main roads and public transport system quickly became clogged as hundreds of people rushed to get to higher ground.
Many high-rise buildings in the city centre were evacuated and office workers were sent home early as the city centre effectively shut down.
Early estimates suggested that more than 9,000 homes could be inundated when the Brisbane River peaks at 12ft over the next two days. Campbell Newman, the Brisbane mayor, said 6,500 homes and businesses could experience seriously flooding.
Brisbane, which is Australia's third largest city and is home to two million people, was under siege on four fronts, with runoff from the flash flooding in the Lockyer Valley, large volumes of water running down the Brisbane River, a king tide and heavy rain combining to create what Julia Gillard, the prime minister, called "a very dire situation".
The threat to Brisbane comes after an inland tsunami swept through Toowoomba, 77 miles to the west of the Queensland capital, on Monday.
Among the dead were four children and entire families were among the missing.
Outside Brisbane, towns to the west and north were isolated by the floodwaters and rescue efforts were being hampered by continuing bad weather. About 300 people were being airlifted from the Lockyer Valley town of Forest Hill and the outlook was poor for the town of Ipswich, where water was rising, affecting 400 streets.
Ms Gillard has said the events unfolding in Queensland were shocking and warned the nation to brace for the death toll to rise.
She fielded questions about whether the region had been properly prepared for the deluge. But government meteorologists have said that the flash flooding was almost impossible to predict.
Anna Bligh, the premier of Queensland, fought back tears as she described the events as "our darkest hour".
"The flood crisis has deepened seriously over the past several hours," she said.
"This weather may be breaking our hearts but it will not break our will."
Ms Bligh warned that the entire city of Brisbane would be affected with workplaces and shopping centres closed. She urged residents to stay off the roads unless absolutely necessary and warned that the death toll could double.
"We are facing one of our toughest ever tests... now is not a time to panic, it is a time to stick together," she said.
As the flooding sweeps across southeast Queensland, bushfires are raging in Western Australia, threatening scores of properties.