Officials said about only 20 buildings in Maryborough, where about 22,000 people live, were expected to be flooded after the river burst its banks in the overnight downpour. The water level is expected to peak on Sunday.
"A number of businesses... will have floodwaters in their basements," Mayor Mick Kruger said.
But the new flooding was a reminder that the state has almost no capacity to absorb more heavy rain after weeks of drenching tropical weather submerged an area the size of Germany and France combined.
Ten people have died since late November and about 200,000 have been affected by the floods. Roads and railway lines have been cut, Queensland's big-exporting coal industry has virtually shut down, and cattle ranching and farming across a large part of the state are at a standstill.
While new rain was causing problems in some parts of the state, officials said a massive relief operation has moved from emergency operations to recovery, as the city of Rockhampton and other towns wait for water levels to drop, and dozens of others begin mopping up sludge.
Prime Minister Julia Gillard flew to several towns cut off by floodwaters or partially underwater today, and sought to reassure residents that their towns would be restored in an operation led by an army general who said it might take years to fix all the damaged roads, railway lines and bridges.
"Until we see these floodwaters recede, we won't see the true extent of the damage," she told reporters in the town of St George.
Queensland Premier has said the price of rebuilding homes, businesses and infrastructure, coupled with economic losses, could be as high as 5 billion dollars (£3.2 billion).
Floodwater draining east toward the ocean was still rising in some places, such as St George, where about 2,500 residents were bracing for the second major flood in less than a year.