Factsheet: Faecal Indicators

Faecal bacteria or pathogens can cause disease in people if they come in contact with them. Pathogens can also accumulate in some types of shellfish, posing a risk to people if eaten.


Faecal contamination in water is monitored using “indicator” bacteria (or microbes) that are present in the faeces of warm-blooded mammals (including people) and birds. The two most commonly measured faecal indicator bacteria are E. coli (in freshwater) and Enterococci (in marine waters).

What is E. coli?

E. coli (Escherichia coli ) is a type of bacteria commonly found in the guts of warm-blooded mammals (including people) and birds. High E. coli concentrations in freshwater can be harmful to humans.

Common sources of E. coli bacteria are untreated human wastewater discharges, stormwater run-off and animal waste.  E. coli survives outside the body and can survive for up to four to six weeks in fresh water making it a useful indicator of faecal presence and therefore of disease causing organisms in a river or lake.  Faecal concentrations are typically higher in pastoral streams but even near-pristine streams are not totally free from E. coli because of faecal deposition by birds and wild animals.

Why is too much E. coli a problem?

Too much E. coli means that the water is unsafe to drink or swim in and can cause infections of ears, eyes, nasal cavity, skin, and the upper respiratory tract. Water is only deemed safe for drinking if there are very low concentrations of E. coli present. When E. coli in rivers and lakes are detected above 550 per 100 mL, health authorities put up signs stating that swimming or collecting shellfish is not recommended. When E. coli concentrations are high, other faecal pathogens can also be present and might cause illness.

How to test for E. coli?

Water samples are collected by your local authority as part of their State of the Environment or recreational monitoring and sent to laboratories to be tested for E. coli using nationally or internationally approved methods. During the summer months (November – March), councils collect E. coli weekly at sites where people swim, and these results are show in the 'Can I Swim Here?' topic.  

Which unit is it given in?

E. coli can be counted under the microscope as Colony Forming Units (cfu) or Most Probable Number (MPN) per 100 mL.



What are enterococci?

Enterococci are bacteria that naturally occur in the gut of humans and animals as well as birds, fish and reptiles. They are the preferred biological indicator for faecal contamination of coastal swimming sites. Enterococci are the bacterial indicator for Marine water.

How to test for enterococci?

Water samples are collected weekly from popular swimming sites by local authorities during the swimming season (usually between 1 November – 31 March), and these results are show in the 'Can I Swim Here?' topic.

Which unit is it given in?

Enterococci are counted under the microscope in numbers per 100 mL.

Where do I find more information?

Ministry for the Environment and Ministry of Health (2003) Microbial Water Quality Guidelines for Marine and Freshwater Recreational Areas. New Zealand Ministry for Environment and Ministry of Health.