One of Melbourne's most popular beaches — St Kilda Beach — has been rated "unacceptable" for swimming today and tomorrow because of pollution.

Only St Kilda Beach and St Helens Beach in Geelong have been rated unacceptable for swimming out of the Bay's 36 monitored beaches.

The Environment Protection Authority said "water quality testing has shown unacceptable water quality due to elevated bacterial levels at St Kilda and St Helens beaches, after heavy rain Sunday night and all day Monday".

"As a result of these levels, EPA advises against swimming at these beaches until further notice. The water has been re-sampled and the information will be updated once results are received," the Authority said in a statement this afternoon.

Unacceptable is the authority's highest rating for water pollution under its beach report monitoring system.

For the rest of today, swimmers were also advised not to swim at The Dell and Queenscliff Beaches, with the water quality rated as poor.