A downpour in Melbourne delivered half of October's average rainfall in one hour.
Some suburbs received 30 millimetres of rain in as little as 20 minutes on Friday.
As of 4.30pm, authorities were concerned about two dams in Craigieburn in the city's north, with fears a large private dam could collapse and impact local roads.
There were also moderate flood warnings for the Murray River downstream of the Hume Dam in the state's north and the Loddon River at Laanecoorie, near Bendigo.
Authorities are bracing for major flooding on Saturday along the Avoca River at Charleton, northwest of Bendigo.
The Friday deluge followed a night of wild weather, with the SES receiving more than 600 calls for help in 24 hours.
The Evoca and Maryborough areas in regional Victoria received 50 to 65mm in an hour, which is roughly one month's worth of rain.
Areas around Frankston, Bayside, Woodend and the Maryborough district were also hard hit.
State Response Controller Tim Wiebusch said he was disappointed at least 15 people attempted to drive through flood waters.
"We know the single largest death or cause of death in flooding is people attempting to drive through flood waters," he said.
"Driving through flood waters could be the last decision you make."
Over half of the calls for assistance related to the impacts of flash flooding such as leaking roofs.
More than 120 requests were for building damage and more than 100 related to fallen trees.
