Health New Zealand - Te Whatu Ora found the bacteria in samples taken from Lake Rua at Roto Kohatu recreation reserve in Harewood.
Medical Officer of Health Dr Cheryl Brunton said water quality at the site is not considered suitable for recreational uses, including swimming, because of the risk to health from the bacteria and other pathogens.
"Eating shellfish from this site should be avoided. If fish are eaten, remove the gut and liver and wash in clean water before cooking.
“In most cases the ill-health effects from exposure to contaminated water are minor and short-lived. However, there is the potential for more serious diseases, such as Hepatitis A or Salmonella infection,” Brunton says.
A number of other popular swimming sites in Canterbury may also have high levels of contamination after the rainfall.
Brunton said people should avoid all rivers and beaches for at least two days after heavy rain. The sites where water quality is affected are listed here and on Environment Canterbury’s website.