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.

EPA's chief environmental scientist Mark Taylor says warnings to stay out of the bay are common after major weather events.

"With heavy rains, everything gets flushed into the river - vehicles, faeces, it all gets into water system and out into the ocean," Mr Taylor said on Wednesday.

"Ultimately it's a health-based warning, for people not to exposed to contamination."

Oil and debris including pieces of wood, may also be found in the water, he said.

Swimming in the impacted areas is not advised for at least 48 hours, to allow 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.

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.

A high of 17C is expected in Melbourne on Wednesday along with light showers in the morning and afternoon.

The rain is expected to cap at 2mm with winds hitting up to 15km/h to 20 km/h.

Australian Associated Press