Yea and Seymour residents have been issued evacuation warnings, as severe weather persists throughout Victoria with damaging winds and hail.
VicEmergency has issued immediate evacuation orders for Yea residents on Mulqueeny Lane, Clarence Way, Newberry Chase and Buckland Court, as well as Miller Street, Loan Street, Whatton Place or Court Street.
The relief centre at Yea Shire Hall will be open from 2pm today.
Meanwhile, immediate evacuation orders are also in place for Seymour residents, with flooding expected to impact Emily Street, Tierney Street, Lesley Street, Tallarook Street, Wallis Street, High Street, Elizabeth Street and Butler Street.
Other streets expected to be affected included Alexander Street, Edward Street, Station Street, Tristan Street, Hanna Street, Jubilee Street and Industrial Court.
A relief centre has been opened at Seymour Sports & Aquatic Centre at Chittick Park.
A flood watch is in place for central Victoria, Gippsland and northern Victoria while the Bureau of Meteorology has reported there will be significant rain moving throughout the state, affecting the north and north east into Gippsland.
Daily rainfalls up to 9am on Monday have reached as high as 181mm at the Wild Duck Creek station at Heathcote, while Redesdale's Campaspe River station recorded 135mm.
Stations at Pyalong recorded 130mm, while Flowerdale recorded 126mm.
Major rainfall is also expected throughout the north-east of the state today.
Courney Hazeldene, Ganado Greys, Marong, said that in addition to the 92 millimetres of rain at her Murray Grey stud, she had also received a quarter of her annual rainfall in two weeks.
"I would say it's probably the worst flood that we've had," she said.
"We've been farming here for 15 years, and it's the most damage that we've ever seen with our fences."
She said most of her fences washed away between 10-11pm, while local creek damage has also had an "unprecedented" impact.
"Every house has a lake frontage now around here," she said.
"You'd only be able to get through your paddocks with a four-wheel drive or a tractor, [while] there's plenty of damage to crops.
"If anyone hadn't got their harvest off, well they're absolutely ruined too.
She said that round bales of hay were also in danger of floating away or severely damaged.
But despite the floods causing significant damage and livestock having to be moved to higher ground, Ms Hazeldene was able to find a silver lining to the wet weather.
"We're actually growing grass now, that just does not happen, ever, in January, in Bendigo."
"It's an inconvenience, and yes, there's repairs to be done, but I say any day I would rather have a flood and some damage then a prolonged drought.
"I've been through that before and I don't want to go through that again, so this is great for me."
Roads have also been affected, with the Midland Highway shut in both directions north of Bendigo due to flooding, with emergency services diverting traffic between Epsom and Goornong.
The Wimmera Highway is also closed between Marong to Newbridge, while the Calder Alternative Hwy to Bridgewater-Maldon Road is closed due to flooding.
The severe thunderstorm warning had been in place for the Ararat, Stawell and Horsham, extending down to Warrnambool.
In the north-east Bogong High Plains Road will be temporarily closed between Mt Beauty and Falls Creek from 9pm, Sunday, January 7.
Emergency Management Commissioner Rick Nugent said there had been more than 38 rescues from floodwaters.
Motorists should not drive through floodwater, and pull over away from trees, drains, low lying areas and floodwater if driving conditions are dangerous.
"If you are leaving, leave early, but if you are staying please make sure you have enough supplies to last three days," he said.
"Cars don't float for very long, and they cause very serious risk to people in them."
VICSES Operations Chief Officer Tim Wiebusch said there could be 200 homes impacted by the floodwaters at Seymour, including a possible 50 homes to experience over-floor flooding.
He said they expected the flooding peak to happen later this afternoon.