Victoria is preparing for potential disaster as barely a patch of the Australian state remains untouched after days of heavy rain this week.

A man is missing and at least 80 Victorian homes are flooded as the state's emergency services commissioner said another 10 were expected to flood overnight.

Although rain has eased, commissioner Craig Lapsley said river, creek and water catchments are swollen to capacity and more rain is forecast next week.

"This is not going away," Lapsley said.

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"We are calling this the floods of September, 2016. We are expecting it to be a significant event."

Despite torrential rain easing, floodwaters continue to rise.

"The state is saturated, we're now seeing most of our rivers in some sort of flood," he said.

Lapsley said with water at current levels, there were concerns about what impact more rain would have.

"Next week's weather is concerning. If we get 20mm when we have reservoirs full, dams full and rivers full, that's a concern," he said.

"That's our next problem to face. We are trying to get a good understanding of the weather and the change in the weather pattern that has potential to bring rain with it."

Lapsley said 188 roads are closed across the state, including the Great Ocean Rd, which is cut in two sections either side of Lorne.

In one of the worst hit areas, the central west town of Charlton, flooding in the Avoca River is expected to peak at 7.5m about 8am this morning, local time.

Lapsley said that meant at least 10 homes in the town could go underwater, adding to the 80 that have been flooded in South Australia.

An elderly farmer whose ute was found submerged by floodwaters in Macarthur in the state's west also remains missing.

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South Australia and Victoria have borne the brunt of torrential rainfalls over the past fees days.

Eighty homes have been flooded and 39 roads remain closed after torrential rain and gale-force winds battered the Adelaide Hills, causing millions of dollars in damage.

But Weatherzone meteorologist Ben Domensino told news.com.au more rain was certainly on the way.

He said the next systems were a cause for concern.

"A cold front moving across The Bight will hit western Victoria on Saturday," he said.

Up to 10mm-20mm of rain is predicted, and Domensino said this would be enough to cause widespread flooding.

"A prediction of 20mm of rain doesn't sound like much, but the concern is these two systems will add to the waterlogged conditions," he said.

"While this is good news for soil moisture levels it, certainly has the potential to be dangerous in the short term due to catchments being so full."

In South Australia, residents began cleaning up yesterday, even as authorities warned that more rain was on the way.

River levels across the Mt Lofty Ranges had peaked, reducing any immediate risk of further flooding, but could be swelled by falls forecast for tomorrow and next week.

Some centres in the Adelaide Hills, on the Fleurieu Peninsula and on Kangaroo Island had their wettest September day on record on Wednesday, copping more than 100mm.

That led to flooding across a wide area with the towns of Aldgate, Bridgewater and Hahndorf and Adelaide's eastern suburbs the hardest hit.

In Victoria, 19 flood warnings are in place for rivers and creeks across the state, and South Australia has three.