A watch and act alert was issued for Mount Martha, Mornington, Hastings and Dromana on Monday morning as heavy rainfall caused localised flash flooding and building damage.
Residents were told to stay inside and away from floodwaters as the severe thunderstorm hit.
Victoria State Emergency Service (VICSES) chief officer Tim Wiebusch said volunteers responded to more than 550 calls for help, of which 318 were for flooding incidents, 104 for fallen trees and 44 for building damage.
He said Mount Martha and Mornington were hit with 40-50mm of rain over the space of a few hours and about 38 inland water rescues were made.
"A range of the rescues this morning have been people attempting to drive through flash flood waters but also (people) seeing water levels rise around their houses very, very quickly," he told ABC TV.
Mr Wiebusch said there had also been significant downpours in the state's northeast overnight, including 60 to 70mm of rainfall in some areas.
There was major flooding at the Murray River in Albury-Wodonga and that was expected to flow downstream to Yarrawonga and Tocumwal as more rain fell.
Mr Wiebusch said flash flooding was expected to turn into major riverine flooding in the coming days as already saturated catchments felt the impact of the extra water.
The Bureau of Meteorology issued severe thunderstorm warnings for parts of central and northeast Victoria on Sunday, including for Rutherglen where 28mm of rain fell in just 30 minutes during the afternoon.
VICSES has received more than 13,500 requests for assistance in the past month since severe flooding hit the state of Victoria.
Moderate to major flood warnings remain current for some parts of the state, particularly along the Murray River including at Kerang, Echuca, Barham, Barmah, Robinvale and Mildura.
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