Warrnambool-based Incident Controller Alfred Mason said flood levels around Port Fairy were falling on Saturday evening after peaking in the afternoon.

"The water is going to take quite a few days to recede. There is an awful lot of water laying further upstream that hasn't come down," Mr Mason said.

He said while water had overflowed into just three homes flooding had affected numerous more properties' gardens, sheds, paddocks and fences.

"In Port Fairy it is one-in-50-year flood is how we are treating it," Mr Mason said.

He said the flood had behaved differently to historic floods.

Moyne River levels peaked at the Toolong gauge north of Port Fairy on Friday night following heavy rain earlier in the week, but water rose further in the town on Saturday morning.

"There was more water coming into town that wasn't coming from the river," Mr Mason said.

He said the water would now take "quite a few days" to recede.

"It will be a big clean up for quite a while for the community. There could be property damage found after the water recedes," Mr Mason said.

"It could be farm fencing, they might have damage to small infrastructure, there's water in garages.

"The worst is over as in the flood level. The bad story is that the clean up for some business, farms and homes is going to be a bit heartbreaking for them."

He asked people not to drive through flood water or on closed roads.

"If a road is closed it's closed. We are asking people not to drive through water. We are again reminding people to be wary of the hazards you can't see," Mr Mason said.

The incident control centre downgraded its warning message to an alert level on Saturday afternoon.

For more information visit Vic Emergency.

Update, 3pm: A PORT Fairy state emergency leader says Saturday's flooding is the worst he's seen in nearly three decades.

Port Fairy SES unit controller Steve McDowell said the impact of the flood water was expected to continue for another 24 hours in the Port Fairy region.

"The evidence is that at the Toolong gauge it has reached its peak. They are predicting the peak in Port Fairy will be sometime this afternoon. And we should see the waters recede hopefully reasonably quickly," Mr McDowell said.

"The tide drops tonight and we are hoping that will allow some of the water to get out into the sea.

"They are predicting it will go for at least another 24 hours."

He said water had overflowed into three houses and "many others" had external outbuildings flooded.

Mr McDowell said areas around Koroit, Kirkstall, Toolong and Port Fairy had been affected.

Port Fairy Gardens Holiday Park evacuated on Friday evening, with flood water impacting a reserve area on Saturday.

But Mr McDowell said the buildings and park had "not been affected at all".

"It's been fairly widespread our response across the last three or four days," he said.

"I've been in the unit 27 years, and this is the worst flood we have experienced in this area around Port Fairy."

Mr McDowell said the flood was another event in a challenging year.

"It's something we didn't see coming. This year has been a bit of a tough year with the fires, then COVID and now this," he said.

"The way the community has come together through this event is really amazing."

Update, 1.30pm: A PORT Fairy couple with flood water lapping into their home say without emergency services working through the night their situation could be far worse.

Pam and Trevor Hockley said the SES crews sandbagged their Griffiths Street house on Friday afternoon, but water seeped into the house around 8am Saturday morning.

Water from the overflowing Moyne River flooded the backyard and entered through a backdoor and laundry door, but living areas in the two-storey home were unaffected.

"We live upstairs and downstairs is a self-contained unit. It's all tiled floor," Ms Hockley said.

"We are just mopping the floor and mopping the floor."

She said emergency services had been at the house since Friday evening until midday Saturday.

"They just did a marvelous job, they're just great," Ms Hockley said.

The couple moved to the house in 2009 and Ms Hockley said floods in 2010 were "nothing compared to this".

"The one in 2010 only just got through the back fence," she said, adding water was about three-feet deep at the same fence on Saturday.

"We have been told it's a flood zone, but didn't ever think it would be anything like this."

The couple did not sleep Friday night and their daughter and son-in-law arrived from Brucknell to lend a hand on Saturday morning.

"I am not going to do any clean up until it's gone out the back fence," Ms Hockley said.

"You just have to take it in your stride, you can't fight it. It's a waiting game."

EARLIER: THREE houses in the Port Fairy area have been inundated with water and emergency services say moderate floods are still rising.

But Warrnambool-based incident controller Alfred Mason said emergency services were "cautiously optimistic" with the Moyne River's Toolong gauge "dropping".

Mr Mason said the control centre believed flood levels in Port Fairy could reach a 10-to-20-year level, with the Toolong gauge reaching a "peak" 4.47 metres at 9.45pm Friday.

"The water coming into Port Fairy is still increasing because it's coming from the floodplain and through other tributaries," he said.

"That's why it is increasing in the town. But the gauge is dropping. It's moving very slowly."

He said three homes in the Port Fairy area were inundated with water, with Griffiths Street, Lydiard Street and Rosebrook worst affected.

"Over the next 10 hours it should get back to a comfortable level," Mr Mason said.

"We believe everything should be OK, we have people now providing hourly reports back because we don't have gauges in town."

He said closer to Warrnambool the Hopkins River was also still "rising slightly" and crews were monitoring for any further flooding in Allansford.

Mr Mason said water levels in the Merri River were continuing to drop.

Emergency services cautioned drivers against disobeying road closure signs.

"We still have trouble with people driving past barriers, which is disappointing," Mr Mason said.

"Some of the roads they are driving through, the properties or the homes are being protected with sandbag levels, and if cars go through the weight will cause the water to go across."

Have you signed up to The Standard's daily newsletter and breaking news emails? You can register below and make sure you are up to date with everything that's happening in the south-west.