Showers and possible hail have been forecast south of the ranges from Tuesday, while isolated thunderstorms could hit northern Victoria before wild weather ramps up again from the weekend.
Multiple Watch and Acts have been issued across the state as the State Emergency Service remains on alert for requests for assistance.
A moderate flood warning has been issued for the Moorabool River at Batesford Bridge in Victoria's southwest, with water levels expected to reach four metres on Tuesday.
Flooding is also expected on the Yarra River from Millgrove to Coldstream and from Coldstream to Warrandyte, with rainfall totals of 15-20mm forecast for the upper part of the catchment.
The Murray River is expected to peak at Wakool Junction, north of Swan Hill along the NSW border, by about midday on Tuesday.
Floodwater is steadily flowing north towards Mildura and is likely to reach the major regional centre by late next week.
Major flooding is also expected at Yarrawonga in the state's northeast on Thursday and further west in Tocumwal by the weekend as floodwaters from Albury-Wodonga head downstream.
Catchments across the state have been full for some time now after record rainfall in October.
Some 85 warnings remain active and almost 450 roads are closed.
Major to moderate flood warnings have been issued for several waterways across the state but Emergency Management Commissioner Andrew Crisp said he did not expect rivers to rise as high as in previous weeks.
On Monday the emergency moved south to the Mornington Peninsula as flash flooding inundated streets, isolated residents and damaged homes across several suburbs.
There were more than 650 calls for help across the state in the 24 hours to Monday morning, with about 300 from the peninsula.
Seven homes in the suburb of Hastings received flooding above floor level, forcing residents to relocate.
In the state's west, six homes were flooded at Lethbridge near Geelong while authorities are still working out how to move heavy machinery onto saturated ground to fix a train derailment at Inverleigh.
The state's Environmental Protection Authority has issued a fresh plea for communities in northern Victoria to stay away from floodwaters after finding low levels of the bacteria E. coli in major waterways at Swan Hill, Rochester and Echuca.
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