The Mary River at Maryborough has peaked at its highest level in almost 60 years.
About 300 homes and 150 business have been impacted by flood waters and a tornado in the town.
Fraser Coast disaster co-ordinator Mal Churchill expects the major flood levels to slowly fall within the next two days and for the recovery phase to kick in.
The peak of 10.7 metres was recorded at 8:00am (AEST).
The record in 1955 was 11.28 metres.
Fraser Coast Mayor Gerard O'Connell says the river rose slowly overnight and residents were prepared.
"High set houses that would have water underneath them, some that would have water through them," he said.
"We spent a good deal of the last couple of days getting the message out to people to self-evacuate, get to higher and dryer land.
"In many cases that's certainly what has happened."
Floodwaters are receding in Gympie and the clean-up has begun.
The Mary River has started to drop after peaking at 20.3 metres in Gympie.
That is higher than the 2011 floods but lower than 1999, when much of Gympie went under.
More than 160 properties are flooded, most of them businesses in the city centre.
Gympie Mayor Ron Dyne says he expects clean-up crews to be able to get into the shops in the main street this morning.
"Some people have started to clean up already [in properties] that were right on the periphery of it," Cr Dyne said.
"We'll have rural fire brigade trucks down there to start hosing buildings out.
"Owners will be there after it's been hosed out, squeegeed out, then the owners get there and they can start re-establishing."
The Bruce Highway and regional roads remain cut but some services have been restored to outlying communities.
Police Superintendent Chris Seng says a decision to reopen may be made later today.
"It'll still depend how long it takes the Mary River to fall," Supt Seng said.
"Also the highway will need to be looked at by the Department of Main Roads and Transport, so it may still be some time before we get to open the highway."
Gympie has now had major flooding four times in three years.
The Bureau of Meteorology says major flood levels are also easing slowly at Miva and Tiaro.
© ABC 2013
12:13 EDT Transition season is well under way across northern Australia with thunderstorms a regular occurrence each afternoon.