More than a dozen warnings were issued on Friday, telling residents in several regions to prepare their homes and evacuate if needed.
One person died in flooding in the state’s north earlier this week.
The storm system has now moved south towards Queensland’s heavily populated southeast, which includes Brisbane.
In February, Queensland was devastated by floods that killed 13 people and inundated more than 20,000 homes. Another nine people were killed in floods in neighbouring New South Wales.
Major flooding was forecast for several rivers on Friday. Residents in Gympie, north of the state capital, were warned to expect flooding for the second time in recent months.
In the February disaster, 800 homes and businesses in the town were affected when the river peaked at 23m.
Mayor Glen Hartwig said they were anxious to see how high the local Mary River would rise this time. If it reaches a peak of 15m, businesses – but not homes – will be affected.
“At 16m, it’s snorkels or nothing,” he told the ABC.
Floods also inundated some towns on Friday in the Lockyer Valley, west of Brisbane, and cut off a major highway.
About 300 homes in the region were expected to be affected, after 68 were inundated in February.
“It is soul destroying – it’s absolutely crushing,” Lockyer Valley Mayor Tanya Milligan told the ABC.
A warning siren sounded in the town of Grantham on Friday, with residents in low-lying areas urged to move to higher ground.
In 2011, the town was devastated by a major flooding event that killed 12 people and was likened to an “inland tsunami”.
The Bureau of Meteorology has warned further heavy rainfall on Friday could also lead to life-threatening flash floods and potential landslides. The system will begin easing over the weekend.
Australians will vote in a federal election on 21 May in which climate change is a key issue.
In recent years the country has suffered severe drought, historic bushfires and mass bleaching events on the Great Barrier Reef.