Professor Mark Taylor, the state’s chief environmental scientist at EPA Victoria, said microbes have made their way into the water system after heavy rains throughout October.
"When there's a flood, often sewerage systems and faeces from domestic animals, agricultural animals and native animals will be washed into the river,” Prof Taylor told ABC.
"You can see that when you go down to the bay. The water's cloudy. It's dirty.
Professor Taylor said keen beach swimmers should take a "precautionary approach" and avoid bay water all-together.
"The pollution — or poor water quality — is moving from upstream to downstream, so it will be some time before the beaches start to display suitable or good quality acceptable for swimming.
"I would wager it's probably not going to be suitable until at least next weekend, until the very earliest," he predicted.
On Saturday, popular beaches in Mornington, Aspendale, Carrum, Seaford, Elwood, Werribee and Clifton Springs were rated as having poor water quality.
The advice remains, if the water looks brown, or like a cup of tea or cappuccino, don't go in!
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