The level of faecal bacteria is at unsafe levels at St Kilda and four other beaches around Melbourne.
Environment Protection Authority Victoria has forecast poor water quality ratings at Port Melbourne, Frankston, Mentone, St Kilda and Werribee South after finding increased levels of enterococci during testing on Tuesday.
Enterococci is an indicator of faecal contamination and threat of illnesses for swimmers.
All five beaches are near large waterways or stormwater drains, which the EPA on Wednesday said served as a reminder to avoid swimming near discoloured water.
Mordialloc, Sandringham and Williamstown are forecast to be fair.
The remaining 28 Port Phillip Bay beaches have good forecasts, as does Warrandyte on the Yarra River.
The warnings come as Melbourne approaches a warm spell, when the city is expected to top 30C each day from Thursday until Sunday.
The EPA advises beachgoers to check water quality forecasts daily or sign up for twice-daily SMS alerts before going for a dip.
