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 has warned of poor water quality in Port Phillip Bay. Credit:Justin McManus

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."