Rain records have been smashed with a Victorian town registering three months worth of rain in 24 hours, as other regional areas are ordered to evacuate rapidly rising floodwaters.
People in Seymour and Yea in the Goulburn Valley were told to leave about midday Monday in an emergency warning.
"If you choose to stay, emergency services may not be able to help you," the alert warned.
Authorities later told residents of Yea it was too late to leave, before residents of Rochester on the Campaspe River were also ordered to immediately evacuate.
About 50 homes in Seymour were at risk of being inundated and floodwaters were threatening to isolate another 140 properties as a seven-metre flood peak loomed.
Relief centres opened at Seymour Sports and Aquatic Centre and Yea Shire Hall with centres in Bendigo, Echuca and Rochester popping up.
Victorian Premier Jacinta Allen said about eight people were at Bendigo's evacuation centre.
Central, north central and eastern parts of the state were put on alert, with major flood warnings issued for the Campaspe River near Bendigo.
Flood warnings were issued for the King River, Fifteen Mile Creek, Sunday Creek and the Goulburn River.
Emergency crews made more than 38 flood rescues in Victoria in the 24 hours to 10am on Monday, bringing the state's total flood rescue count to 58 since January 1.
There were 920 calls for assistance to VICSES over the same period for flooding, trees down and building damage, bringing the total to 1200 since 7pm Sunday.
"Cars don't float for very long and they end up causing serious risk to people in them and can potentially cause loss of life," Emergency Management Commissioner Rick Nugent said.
Flash flooding occurred in the state's southwest while more than 180mm of rain was recorded in the central Victoria town of Heathcote, amounting to three months' worth in 24 hours.
Redesdale's more than 117mm in 24 hours was a daily record for any month, from 120 years of data. The 92mm recorded in Bendigo broke 90-year records.
Towns in central Victoria endured an intense 24 hours as the region faced its fourth major rain event since Christmas, the City of Greater Bendigo's acting chief executive Brian Westley said.
"We've got very saturated grounds, we've got full water catchments and we've got full river systems," he told AAP.
"Further rains will result in some level of flooding."
About 30 homes in Goornong, about 30km northeast of Bendigo, and six homes in Redesdale were evacuated after water inundated the properties.
The focus turned to other areas across the state as more flooding was expected over the next 72 hours, VICSES chief operations officer Tim Weibusch said.
Up to 35 houses face being flooded and another 250 could be cut off in Rochester as floodwaters are expected to reach 114.8m on Tuesday.
Kialla, Mooroopna and nearby Shepparton were on alert for minor to moderate flooding.
Wangaratta and Echuca were also warned of the flood risk for the coming days.
People in metropolitan Melbourne were urged to avoid bike and walking paths near the Maribyrnong, Yarra and Bunyip rivers.
Rain has affected water quality as road dirt and grease, animal faeces and vegetation make their way into the Victoria's waterways and increase the risk of gastro or skin rashes.
A trough was expected to move east into southeast NSW and continue along the coast over coming days bringing heavy rainfall, the Bureau of Meteorology's Miriam Bradbury said.
Sydney, the Illawarra and Newcastle should expect moderate to local heavy falls, although they're likely to be tied to thunderstorm activity.
