Fraser Coast Regional Council says the Mary River flood peak will be higher than expected in Maryborough.
Mayor Gerard O'Connell says the river is now expected to rise to around eight metres early tomorrow morning, and a high tide will hit around midnight.
Nine low-lying businesses have already been flooded to varying degrees.
Councillor O'Connell says properties in Maryborough near the Lamington Bridge, in lower Kent Street precincts and around The Pocket area will probably be affected.
"If the Bureau of Meteorology's predictions stay as they are, we're probably looking at in the vicinity of about a dozen businesses and 15 possible homes that could be affected," he said.
"Now when I say affected, that does not necessarily mean that floodwaters will go through the home - it just may mean that floodwaters will come into the property."
He says many of the businesses were hit in the Australia Day floods and one of the owners was in the process of rebuilding.
"The marina businesses ... are well prepared," he said.
"In fact, the marina businesses I'm referring to, the building that they occupy, never got reoccupied since the last flood, so it's a shell of a building."
Local disaster coordinator Mal Churchill says it is very tough for businesses yet to recover from the Australia Day flood.
"A lot of the recovery work was progressing and certainly starting to move forward and now you have this impact," he said.
"It will probably set them back for a little while, but we just keep urging them to hang in there and this will pass in the next three days."
He says residents in flood-prone areas are being advised to leave as a precaution but there is no reason to panic.
"Be prepared in the event that they do need to evacuate - it's probably easier to go early than leave it until too late," he said.
"There's a history of flooding in Maryborough and a lot of these residents are well aware of what they need to do.
"The last thing we need is for panic - the previous flood here went to just under 11 metres."
Meanwhile further north, weather bureau forecaster Peter Otto says Bundaberg will miss out on the worst of the rain today.
"There is some rain areas around to the north of Bundaberg and just catching Bundaberg on the side of things just at the moment," he said.
"It might cause some concern to residents, but the hydrologists don't believe it's enough to add significantly to the river levels, so things are easing off."
© ABC 2013
07:23 EDT A Western Australian farmer is surveying damage after a freak storm ripped through parts of his property.