Raised E. coli counts have raised red warning flags over eight of the city's 11 lakefront beaches.
"The other day we saw a huge explosion of sewage from the city discharged into the rivers ... and into the harbour," said Mark Matson of Lake Ontario Waterkeeper.
The shutdowns stretch all the way from Marie Curtis Park in Etobiocke to the Rouge Beach in Scarborough.
Safe E. coli levels are normally below the 100 level — but Sunnyside Beach on Thursday the E. coli levels were measured at 1,784.
Even the beaches on the Toronto Islands have been closed, which is a rare occurence.
"In my experience I've never seen E. coli or bacteria at those numbers on Toronto Island beaches," said Matson.
A few swimming areas are still safe, including Woodbine Beaches, Kew Balmy Beach and Bluffer's Beach Park.
Cameron Powell, the head lifeguard at Cherry Beach and says the warnings are not common.
"Usually, it's clean most of the summer." he said. "It's just the storm brought everything up."
The city's beaches are undoubtedly clean, says Powell pointing to the international blue flag system the city uses to monitor the lake water.
"It's a bit of a bad reputation. On most days it's really good."