The City of Victor Harbor has closed the Encounter Lakes and Franklin Island Waterways after routine testing found high levels of a faecal indicator bacteria.

The lakes and waterways cannot be used for swimming or other recreational uses while the closure remains in place.

The council says scheduled testing showed readings higher than the guideline value for Enterococci faecalis (a faecal indicator bacteria) in more than one location in the Encounter Lakes System.

Symptoms of Enterococcus faecalis infection can include fever, chills, fatigue, headache, nausea, abdominal pain and vomiting.

Council intends to flush the lakes as soon as tide levels permit and continue to undertake testing.