The Bureau of Meteorology says moderate flood warnings are in place for the Bemm, Cann and Genoa Rivers following heavy rainfall in East Gippsland yesterday.
A minor flood warning is also in place for the Snowy River.
Widespread falls between 70 to 110mm were recorded yesterday, with Mount Waldron recording the highest total of 135mm.
The gorge on the Genoa River recorded 114mm while Chandlers Creek saw 110mm fall.
Senior Forecaster Tom Delamotte said rainfall had mostly eased around Gippsland for today.
"There's still a few showers to come but only expecting further falls of around 5mm or so for the rest of today," he said.
"By tonight we should see dry conditions prevail over Gippsland."
He said the weather would be briefly settled around the state for the rest of the day, but there was another cold front expected to move through tomorrow afternoon and evening.
"Do expect to see some showers developing from the west on Thursday and also a return to some colder conditions following that front," he said.
He said the cold front was not expected to bring as much rain as what had been experienced in East Gippsland this week.
"As we transition into more of a westerly flow with the cold fronts moving through the end of the week, we're going to see the highest falls occurring about the south west of the state and also about the Yarra Ranges and around the Mount Baw Baw area into West Gippsland," he said.
"Not nearly as much rainfall, and also expecting heavier falls over a different part of the state."
He said the flood warnings were likely to remain in place until towards the end of the week.