Widespread showers and storms on Sunday could cause moderate to major flooding across areas in the state's northeast, which are expected to receive 60-90 millimetres of rain.
Heavy rain and large hail pose a threat to the rest of the state, while parts of Melbourne and Riverine communities could also experience flash flooding.
A flood watch has been issued for more than 25 rivers and 45 warnings remain active.
Communities most at risk include Benalla, Wangaratta, Wodonga, Yarrawonga, Tocumwal and Shepparton.
It is feared water could rise to about the same level as the devastating 1975 floods in low-lying areas along the Murray, such as Mildura, Robinvale, Boundary Bend and Wakool Junction.
The Hume Dam is already at 96 per cent capacity, prompting authorities to release 95 gigalitres per day.
Murray–Darling Basin Authority executive Andrew Reynolds said the operation was a delicate balancing act between freeing up space for future rainfall while minimising the impact on communities downstream.
Victoria SES chief operations officer Tim Wiebusch said almost every water storage facility in Victoria was at capacity and flooding could continue for another six to eight weeks.
"We can't emphasise enough that this flooding emergency is continuing, people need to remain alert to their conditions," Mr Wiebusch told reporters.
Below-average temperatures are expected to set in next week, creating snow in Alpine areas.
There have been about 14,000 calls for help to the SES since the disaster began about a month ago.
About 150 people and pets impacted by flooding are living at the Mickleham Quarantine Facility.
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