Authorities are warning major flooding is likely to hit regional Victorian city of Shepparton by Saturday evening, with predictions it could exceed 1974 flood levels and reach up to 12 metres.
Houses could be impacted and key roads may be cut off.
Hundreds of regional Victorian residents have fled their homes, with evacuation warnings issued for Charlton, Wedderburn, Murchison, Rochester and low lying parts of Benalla and Maribyrnong.
Authorities say the north-central Victoria town of Charlton is set to hit by flooding for three to five days, with 40 to 50 homes likely to be inundated on Saturday. It could result in 70 per cent of the town going under water.
Murchison residents are facing record-level flooding of the Goulburn River, which may reach around 12 metres by Saturday afternoon.
Rochester and Seymour continue to be priority focus areas for authorities.
Flood levels in Seymour have peaked above record levels recorded in May 1974.
Emergency services have warned worst-case river rises in Rochester could result in a one-in-200-year flood event.
Residents in low lying areas of Skipton, west of Ballarat, have been told to move to higher ground as the Mount Emu Creek continues to rise to a predicted major flood level of 5.7 metres, cutting the town in half.
Premier Daniel Andrews confirmed on Friday 500 homes have been flooded across Victoria, and another 500 homes are isolated.
"That number will definitely grow," Mr Andrews said.
A man who was reported missing to the State Emergency Services in floodwaters at Newbridge, west of Bendigo, has been rescued by police.
A Victoria Police spokesperson said the man ignored a roadblock and drove his car into floodwaters and he was rescued clinging to a tree branch.
Victoria Police has revealed the details of a rescue of a woman in her 70s, trapped in flood waters on the Pyrenees Highway near Newstead on Thursday afternoon.
A local police member waded through flood waters and floated a rope to the woman, allowing her to secure herself to a tree until the swift water rescue team arrived.
Rescuers have responded to more than 2,500 requests for help since the rain set in on Thursday.
More than 200 motorists have been rescued from floodwaters, and almost 4,500 houses were still without power at midday.
Horses rescued from neck-deep water
Just north of Seymour, there were concerns for the safety of hundreds of racehorses trained across the region.
One racehorse owner put a call-out on social media for anyone with a float or horse knowledge to help evacuate the animals.
On Friday morning, volunteers jumped in dinghies and swam with some of the horses to higher ground, with staff herding the horses across internal roads.
Tony Stephens, from a stud farm at Mangalore, said he faced a "pretty devastating emergency".
"The waters are still coming up, it's pretty swift … it's a matter of trying to get as many horses [as possible] to safety at the moment," Mr Stephens said.
Overnight rescues in Seymour
The Goulburn River in Seymour has broken its banks and dozens residents have been rescued by boat from their homes and a local motel as floodwaters inundated the town.
Around 300 properties have been impacted.
Planned events across the state have been cancelled, including the Charlton Show and the Avoca Cup.
Transport department is continuing to warn drivers to avoid floodwater, and with the extent of damage to the roads unclear.
Barwon Water is responding to sewer overflows in Geelong, the Surf Coast and Colac, urging residents to avoid flooded areas as workers test for contamination.
The SES says the peak at Euroa has hit, with around 20 properties affected.
On the Broken River at Benalla, a peak similar to that seen in 1993 has seen more than 50 properties flooded.
Surrounding waterways are likely to affect Numurkah and Nathalia in the coming days.
A large sinkhole has also opened up in Echuca as a result of a burst water main.
V/Line has suspended all train and bus services on the Shepparton, Seymour, Albury, Echuca and Swan Hill lines.
Stranded passengers Thursday night were offered emergency accommodation when the decision was made to halt all public transport due to flooding.
'We're not leaving'
Not all residents in Rochester were heeding the warning of the SES.
Therese and Craig Mann made the decision to stay at the Criterion Pub as floodwaters lapped against the pub's front door.
"We're going to save it, because we've got no insurance," Mr Mann said.
"It's our life. We live here. We support our family from here. Everybody that works here is family - it's not just us that's going ot miss out it's our family that work here."
Rain could persist for two months, commissioner says
Even though rainfall was expected to ease on Friday, residents were warned waterways would continue to rise, and flood risks may continue across the state for up to two months.
Mr Crisp parts of the state would see "above average rainfall for the next six to eight weeks".
"There is every chance we will have another weather event next week," he said.
"We will get through certain spike periods but there will be more to come."
At Marong in central Victoria bridges had been cut off by floodwaters, leaving just one access route to the city of Bendigo.
Marong publican Jake Lougoon said lots of young families who had recently moved into the area had never seen flooding like this before.
"A group of 10 locals … went down to the lower side of Marong and they're loading fridges, appliances, furniture … into trucks to help people get away from the floods," he said.
"Luckily we've got a good community here and everyone is here to support each other."
At Echuca on the Murray River residents are being told to boil their drinking water because tainted stormwater has entered the town's treated water system.
