There were more than 300 requests for assistance to the State Emergency Service overnight, mostly connected to flooding near Eildon.
A farmer had to be rescued from floodwaters in Alexandra after he got into trouble on a tractor while attempting to rescue cattle, police said.
Footage from the incident shows the vehicle stranded in gushing water metres away from what appears to be a dirt road.
The 43-year-old Alexandra man suffered non-life-threatening injuries and was taken to hospital.
Fires at Briagolong and Loch Sport have been downgraded to an advice warning with the focus firmly on areas at risk of flooding after a deluge on Tuesday and Wednesday.
Watch and act alerts for flooding were issued across eastern Victoria for as far north as the King River at Cheshunt and south to Glenmaggie.
Residents along the Acheron River near Marysville and the Goulburn River near Lake Eildon were warned moderate flooding was expected after 140mm of rain fell in 24 hours.
An alert was also issued for parts of the Yarra River on the outskirts of Melbourne.
Emergency Services Minister Jaclyn Symes said the situation was dynamic.
"We have, in good news, downgraded emergency warnings for fire," Ms Symes told reporters at state parliament on Wednesday morning.
"We've had a lot of rain across the state and that has brought flood concerns and flash flooding concerns."
The Bureau of Meteorology placed Melbourne and most of the state's east under flood watch with more rain expected throughout Wednesday.
Energy Minister Lily D'Ambrosio said the government was working closely with providers to ensure the wild weather and natural disasters had a minimal impact on energy supply.
Weather conditions were expected to ease from Thursday but flooding was tipped to last until the weekend.
The flood threat comes after many residents in Gippsland were put on alert for fires.
About 700 firefighters spent three days battling two separate blazes, with one home lost in Briagolong but no reports of serious injuries.
The cause of that blaze, which grew to about 17,500 hectares, is under investigation.