The City of Hamilton is advising residents to avoid contact with the water in Chedoke Creek and Cootes Paradise due to a high level of contamination.
The city says the source is unknown.
Crews are inspecting sewers and looking upstream for the potential cause.
The Royal Botanical Gardens (RBG) has removed the docks at Cootes Paradise.
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Warning signs are being installed at public access points along the shoreline of the affected area.
Public Health Services says warm water and soap should be used to wash off if water from the contaminated area comes in contact with skin.