Gannawarra Shire Mayor Charlie Gillingham said water near Kerang and smaller surrounding towns was already high as of Saturday morning with the peak expected in coming hours.
"We've got water coming in from everywhere," Mr Gillingham told AAP.
He said the Kerang levee was successfully holding water back but he expected it might not recede for a month or more.
Rain and thunderstorms returned across the state overnight while western Victoria experienced the brunt of wild weather.
The SES received about 140 requests for help across the southwest from Geelong to Hamilton.
Three people were rescued after driving through floodwaters in Geelong and more than 85 millimetres of rain was recorded in nearby She Oaks.
"We can't emphasise enough - do not drive through flash floodwaters. It could be the last decision you make," Tim Wiebusch from SES Victoria told Seven's Sunrise.
The SES has received more than 8300 calls for help since the weather emergency began and more than 750 flood-related rescue requests.
Mr Wiebusch said there was a risk of flash flooding in metropolitan Melbourne as storms set in on Saturday.
It's still a waiting game for residents in Echuca and the smaller towns of Barmah and Lower Moira, with the Murray River yet to peak.
Authorities predict the river will reach levels just below the 1993 flood record overnight on Sunday and into Monday.
Flood warnings also remain for towns along the Loddon, Goulburn, Campaspe and Avoca rivers, with more rain and isolated thunderstorms forecast for the weekend.
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