Melburnians looking longingly at the warm-to-hot weather forecast for this weekend had better hope for no deluges of rain before then, or swimming will be off limits at the city's beaches.

The Environment Protection Authority says last Thursday's heavy rains swept faecal matter from roads and waterways into city beaches.

The pollutants were so significant that they made the water from Frankston to Werribee South unsuitable for bathing.

Then, after the waters on the Bellarine Peninsula were deemed safe for swimming on Sunday, overnight rainfall saw warnings upgraded, with swimmers urged to be cautious about bathing at beaches between Geelong and Queenscliff.