Waters tested at St Kilda, Port Melbourne, Frankston Life Saving Club, Mentone and Werribee South - all located near storm water outlets or large waterways - were declared "poor" and unsuitable for swimming by the Environment Protection Authority on Wednesday morning.

By Wednesday evening, the water at St Kilda and Werribee South beaches had been declared "fair" rather than "poor".

EPA group manager of applied sciences Dr Anthony Boxshall said the authority would test daily, instead of weekly, until it could be declared safe for swimming.

"We will be taking daily samples until the sampling shows that we are getting a good sense of it (pollutants) dying off or if we find there is some other underlying issue," Dr Boxshall said.

The poor water quality is the result of storm and floods on Thursday last week which pushed storm water into Port Phillip Bay, bringing with it animal and human faeces.

After the storm, beaches from Frankston to Werribee South were initially said to have had "poor" quality water and be unfit for swimming, but by Tuesday the forecast declared those beaches to have improved to be "fair" based on atmospheric and weather conditions.

On Tuesday, Dr Boxshall said the "fair" forecasts on Tuesday were based on decades of data which showed that most pollution would dissipate in 24 to 48 hours. But the one-in-100 year storm, and subsequent "dribbling rain" earlier this week, had shown some beaches had not bounced back as quickly as expected.

"This is effectively science in action and this event will now feed into our data to help us with forecasts into the future," Dr Boxshall said.

"For some areas, this was a one-in-100 year storm with a prolonged period rain afterward," he said.

He said it was unsurprising that the problem beaches were located near to storm water outlets and waterways.

The new preliminary results have given 13 beaches a clean bill of health. Three other beaches - Mordialloc, Sandringham and Williamstown -  remain as only "fair" meaning there is still some risk of swimmers getting sick.

The EPA test the waters for increased levels of enterococci, a group of bacteria found inside warm-blooded animals, including humans.

"Enterococci is recognised as the best indicator in measuring faecal contamination of marine recreational waters," an EPA statement said.

The testing comes as Melbourne's weather is set to warm up with a forecast of 29 degrees predicted on Wednesday and forecast temperatures climbing to 36 degrees on Saturday.

Signs warning swimmers of the dangers have been put in place by local Surf Lifesaving Clubs. The EPA also reminded swimmers to avoid discoloured water.

The EPA is also investigating unconfirmed reports of a dark stain near a storm water outlet on the beach near Port Melbourne's Station Pier.

The patch of questionable water at Port Melbourne. Photo: Justin McManus

The authority is looking into it and says beachgoers should avoid contact with the water.

The EPA called for swimmers to look for signs of stormwater pollution before swimming, including flowing drains, discoloured water, odour and litter along shorelines. It says these are all signs the beach may have poor water quality. But at 1.30pm on Wednesday no signs warning swimmers were erected at the St Kilda Surf Lifesaving Club.

The storm water drain at St Kilda beach on Tuesday. Photo: Leigh Henningham

The news is much better for the rest of Port Phillip Bay where 28 beaches have been declared "good" for swimming with good water quality.

On Tuesday, Launching Place was forecast to have good water quality but after preliminary testing on the Yarra it was declared only "fair" with still some risk of illness to swimmers. Healesville and Kew remain only fair. Warrandyte is rated good for swimming.