Victorians have been urged to steer clear of all Melbourne beaches after the city received one month's worth of rain overnight, washing faecal matter into the bay.
The Environment Protection Authority on Monday gave all of Port Phillip Bay's 36 beaches a "poor" water quality rating.
EPA group manager of applied sciences Dr Anthony Boxshall has predicted the situation could last several days after up to 50 millimetres of rain was dumped on Sunday night.
"The bay is like a shallow tub and all the catchments drain into it," he said. "The water stays in the bay for quite some time just because it's got that little entrance so there's not much exchange."
Popular inland swimming locations along the Yarra River in Kew, Healesville, Warrandyte and Launching Place are also off limits.
While Monday's temperature has hovered around a cool 18 degrees, the weather will be back to 34 degrees by Wednesday.
But Dr Boxshall said beachgoers risked both gastro and infection if conditions hadn't improved by Wednesday.
"It's gastro that we're worried about and infections. If someone had an open wound on their hand, you can get pathogens."
"For people who are fit and healthy, it's not such a big thing, but for some people like kids, older people who are more frail, pregnant women, people who for whatever reason their immune system might be more sensitive, gastro can be more serious so we issue these alerts."
Beaches further afield, such as Lorne and Lakes Entrance, will also be be unsafe for the next 24 hours but are expected to bounce back quicker if there is no more rain.
"I wouldn't be surprised if this was a big event. We know from the last storm around Christmas and New Year that big events tend to last a bit longer," Dr Boxshall said.
"What we know historically is that in 24 to 48 hours the system bounces back. We kind of expect it's on that scale."
The warning comes after wild weather battered the state on Sunday night, with major train and tram delays and more than 5000 homes losing power.
