The wild weather affected 12 council areas, with 102 roads shut, seven schools closed and 14 bus routes disrupted on Wednesday. Emergency services conducted 11 rescues in floodwaters.

A 50-kilometre stretch of the Great Ocean Road, between Moggs Creek and Skenes Creek, remains closed due to a series of landslips and fallen trees.

Ballarat has experienced it wettest three days since 1921, while Beaufort received the most rainfall it's had in a 72-hour period since 1911, and Wedderburn since 1916.

Premier Daniel Andrews said residents near the road faced an "uncertain evening" on Wednesday.

"There's some potential for more serious landslips," he said. "Safety has to come first."

The Victorian State Emergency Service has issued a watch and act alert for the surrounding area.

"Further landslides may occur with current weather conditions, and the threat will remain once rain and showers have past," the alert said.

"It is recommended that all non-essential travel is postponed."

The beachside town of Lorne can be accessed via Deans Marsh-Lorne Road.

Most areas in Western Victoria received their average September rainfall in the three days since Sunday, with Clunes, Ballarat and Mount William in the Grampians being battered with more than double.

Emergency Management Commissioner Craig Lapsley said significant rain started last Friday in south-western Victoria.

He said Carisbrook and Maryborough had been affected from Tuesday night.

He said a swift water rescue was carried out on Wednesday afternoon near Maryborough in which two people were found on the roof of a car that had been driven into water. A helicopter was sent to rescue them.

In Hamilton, which has had almost double its September average rainfall this month, residents in three streets were forced to evacuate as water spilled over the Grange Burn levee on Wednesday morning.

Parts of the surrounding area was left under water, including a park.

The SES earlier sent out an evacuation alert to the entire town.

Southern Grampians Shire Council chief executive Michael Tudball said residents panicked as the council immediately set up a relief centre inside Hamilton's leisure centre.

However, he was "quietly confident" two temporary levees on the Grange Burn catchment would not break.

"It was a bit of a scare when the emergency alert message went out to all of Hamilton," Mr Tudball said. "I'm not sure what happened there."

Blue Malt Restaurant and Beer Lounge manager Afton Barber said business was slow but it was due to the rain rather than the flood.

In nearby Coleraine, RSL Club secretary Eileen Broadwood said the town remained in fear the levee would break after the town was evacuated on Friday.

"It's a bit frightening," she said. "You can't fit much more in the creek I'm afraid."

Ms Broadwood said a member of the club and his disabled wife had lost their home and car in the floods.

"They are emotional. His wife is a real wreck," she said. "But we're trying to help where we can."

Another family lost a car and four rooms of furniture and a caravan park had also be flooded, Ms Broadwood said.

Flood warnings are in place for Glenelg, Loddon, Goulburn, Murray-Riverina, Hopkins and Avoca, Barwon and Werribee rivers.

The SES received more than 440 calls for help from across Victoria on Wednesday, with 242 about flooding.

"Our main concern is keeping an eye on the waters rising in the west of the state," a spokeswoman said. "We're also keeping an eye on the Great Ocean Road area, after a landslide there."