The towns of Myrtleford and Euroa have been told to prepare to evacuate after the area received a season's worth of rain in a day.
Locals are preparing by sandbagging their homes while some have already fled as rivers and creek bulge.
This north-east alpine area has copped the heaviest rainfalls since the storm arrived on Friday, with 170mm recorded at Euroa and 200mm at Strathbogie.
Premier Daniel Andrews urged all Victorians to stay vigilant and look after each other, particularly those in the flood-threatened centres.
"Some of these rainfall totals we've seen are well and truly an entire summer's rain almost in just a 24-hour period," he told reporters in Melbourne.
"That is unprecedented and it really has put a significant strain on many different communities.
"Make that phone call, look out for loved ones and be as well informed as you possibly can."
Rainfall had eased in most areas on Saturday but the Bureau of Meteorology warned it was likely to pick up again in the evening.
"The north-east is expected to get another 30 to 50mm. That will really add to where the ground is saturated," the bureau's Victorian manager Dr Andrew Tupper said.
The SES has received more than 1300 calls for help so far, roughly half of them in the Melbourne area.
Heavy rain splashed parts of Melbourne on Friday and overnight but the city was spared the brunt of the rain.
"The worst of it in Melbourne has passed but there are still risks," Mr Andrews said, reminding people to avoid floodwaters and be safe on the roads.
Several major roads have been closed across Victoria because of the rain, including southbound stretches of the Hume Freeway.
Amid the drama on Friday night, an elderly couple became trapped in their car in floodwaters near Seymour before they were rescued by a farmer in a tractor.
The storm has lead to the cancellation of a number of major events, including the Great Victorian Bike Ride and Taste of Melbourne.
