"It is everything that washes in from the streets, and everything that comes out through the storm water system."
Swimmers who ingest contaminated water have a higher risk of getting gastroenteritis and other illnesses, particularly the elderly and children.
Beaches on the Mornington Peninsula south of Frankston are still suitable for swimming.
Dr Boxshall says the water should clear up in 24-48 hours if it doesn't continue to rain.
More tests will be conducted this week and results posted on the EPA website.
The Bureau of Meteorology forecasts a maximum of 19 degrees on Monday, with light drizzle in the morning and evening.