Parts of Victoria are facing an anxious wait for possible flooding, as heavy rain continues to fall across the state.

Almost all of Victoria is bracing for flash flooding, with warnings covering the entire state except for Gippsland.

Up to 100 millimetres of rain is expected to fall in north, west and central Victoria.

The State Emergency Service (SES) says if the predicted rain fall does hit the region, river levels will be higher than the floods that hit Victoria in September.

SES Spokesman, Tim Wiebusch, says communities along the Loddon, Avoca, Wimmera and Campaspe are particularly at risk.

"If we do see the higher end rainfall totals we will see those rivers go into a higher level than was seen back in September, which was major flooding," he said.

"This will see communities put at risk again of properties being inundated by flood water."

Residents in Halls Gap, Kyneton, Beaufort, Warracknabeal and Dimboola have spent Thursday sandbagging homes and businesses.

Locals are also bracing for flash flooding in Charlton and Glenorchy, and community meetings are planned in several towns.

There has been some minor flooding in Ballarat and near-by towns, and a caravan park near Bendigo was evacuated.

The tiny town of Natimuk is assessing the damage after flooding forced twelve homes to be evacuated on Wednesday.

But locals are reluctant to clean up, because more flooding is likely in coming days.

Phil King from the Weather Bureau says tropical conditions in Victoria in the past few days have brought falls of up to 200 millimetres in some areas.

He says the weather system moving through Victoria on Thursday night will also bring strong, gusty winds.

"We're expecting gusts of up to 120 kilometres around the ranges and 90 kilometres an hour through most of the west and central areas of the state," he said.

Premier, Ted Bailleu, is urging Victorians not to be complacent.

"Victorians do have to be aware that the weather system that is affecting eastern Australia is affecting Victoria as well," he said.