In the last three days SES has responded to over 1500 calls for help, mostly for flooding.

"Over 600 of those were for flooding and almost 500 were for building damage, water coming into buildings. Particularly when gutters were overflowing," she said.

They did more than 40 rescues from cars submerged in water, with 20 rescues on Friday evening in metropolitan Melbourne.

"We're not expecting anymore," she said.

The Bureau of Meteorology predicts an 80 per cent chance of rain in Melbourne on Sunday, with possible thunderstorms in the morning or afternoon.

Flood warnings have been issued for Avoca River and Kiewa River and flood watches for Greater Melbourne, parts of West and South Gippsland, Goulburn and South West Victoria as well.

"We encourage the community to keep an eye on weather warnings because the situation can change," Ms Davie said.

Emergency Management Commissioner Andrew Crisp said the SES had received more than 1400 calls for help during the past 48 hours, many from those who had become trapped in their cars after driving into floodwaters.

Emergency Management Commissioner Andrew Crisp warned people on Saturday not to drive into floodwaters, after criticising drivers who had done so on the Hume Freeway during the deluge on Thursday.

"We saw on the Hume Highway itself … eight trucks and 40 vehicles that found themselves inundated, trapped in water,” he said.

“People who do continue to drive into flash flooding, into water, are putting themselves at risk, making foolish decisions and putting our emergency services at risk.

“I don’t shy away from that warning.”

The Environment Protection Authority continues to warn people against swimming in any beaches around Port Phillip Bay after the deluge.

Beaches from Werribee to Brighton Lifesaving Club, Beaumaris to Aspendale and Seaford to Frankston are rated as being poor due to storm water and possible pollution, with others rated as fair.