The Environmental Protection Agency has rated the water quality at 36 bay beaches near Melbourne and surrounds as "poor".
Impacted beaches stretch from St Kilda and Brighton to the Mornington Peninsula's Portsea, Sorrento and Rye along with Williamstown and Altona in Melbourne's west.
Several beaches past Geelong including Portarlington and St Leonards were given a 'fair' rating which means stormwater pollution is possible.
Water quality in the Yarra River was also given a fair rating on late Tuesday.
It will take at least 48 hours for contaminants to settle in the Yarra after torrential downpours. (Con Chronis/AAP PHOTOS)
Swimming in the impacted areas is not advised for at least 48 hours, in order to give time for the contaminants to settle.
It comes after Melbourne was hit by the equivalent of one month's rain on Monday, while some parts of Victoria recorded rainfall not seen for more than 150 years.
More than 500 calls were made to emergency services, there were 267 reports of building damage and 117 flood-related incidents across the state in the 24 hours to 8am on Tuesday.
One of the worst incidents involved a woman who could have drowned in the central Victorian town of Daylesford.
The 58-year-old fell down an embankment and into a stormwater drain on Monday night.
She was carried by fast-flowing water until grabbing hold of a metal pole but her cries for help could not be heard over the sound of rushing water, Victoria Police said.
The woman suffered minor cuts and bruises but was eventually able to climb out and seek help from a friend.
Areas hardest hit included suburbs in Melbourne's outer east and west, as well as parts of Geelong.
The highest rainfall totals were in central Victoria, while Olympic Park in Melbourne recorded 53mm - more than the city's average rainfall total for the entire month of April.
The wet weather also shattered several long-held daily rainfall records.
Falls in Mornington totalled 65.2mm, the highest daily April rainfall in 157 years.
Wonthaggi in Gippsland received 64.4mm, breaking a record set 114 years ago.
The 92mm at Upper Plenty in Melbourne's northeast was the highest ever recorded at that station.
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