The Environment Protection Authority (EPA) in Victoria is forecasting poor water quality at 21 of the 36 beaches it checks in Port Phillip Bay.
Contaminated water can cause gastroenteritis - a stomach bug - especially in children and the elderly.
A "poor" quality forecast equates to an illness risk of between 5% and 10%.
Australia's public broadcaster ABC said the risky beaches run from Werribee South in Melbourne's south-west to Frankston, about 40 kilometres south of the city's Central Business District.
Dr Anthony Boxshall, the EPA's manager of applied sciences, told ABC News 24: "We have indicators we look for (in water tests), which is an indicator of faecal contamination, which is a really nice way of saying poo."
"It's bird poo, it's horse poo, it's cow poo and it's people poo.
"It is everything that washes in from the streets, and everything that comes out through the storm water system."
Sydney beach bans alcohol after Christmas party
Six found safe after record Australia rain
Man 'fishing' in floods delights Australia
Car-climbing seal back in Australian wild
Dr Boxshall said the water should be back to normal within around 24 to 48 hours, unless there is more rain - which forecasts suggest is possible.
EPA Victoria publishes alerts on its website to help beachgoers around Port Phillip Bay avoid hazards like sewage spills and jellyfish.
It plans to conduct more tests this week and post the results online.
Swimmers are being warned to avoid some of Melbourne's most popular beaches, after torrential storms washed faeces into the water.