Faecal Source Tracking


This framework of tools is used to identify the source of pollutants in a waterway that has become contaminated with faeces. 


The framework of tools has been developed and used by the Institute of Environmental Science and Research New Zealand (ESR). The framework was developed to address the need to identify the source of faecal contaminants in waterways with high E. coli levels. The need to identify source of contaminants arose from a management and mitigation perspective allowing a focus to be placed on the clean-up of those waterways by directly reducing the source of such waste.                                

The ESR framework uses a range of methods to identify the source of faecal contaminants;

  • PCR Markers – species specific microorganisms which are present in faeces are extracted from water sample and analysed using the polymerase chain reaction (PCR) for DNA from source-specific organisms.
  • Faecal Sterol Analysis – Analysis of the sterol composition of animal faeces can generate a sterol fingerprint, which can be distinctive, particularly, when discriminating human faeces from other sources.
  • Fluorescent Whitening Agent Analysis – Analysing for the presence of fluorescent whitening agents (FWAs), present in household washing powders and detergents, indicates the mixing of the source waste with grey water which is common practice in household plumbing systems. The presence of FWAs with the contaminant the indicates human effluent.
  • Library-Based Methods – individual colonies, usually E.coli, are isolated from the sample and ‘fingerprint’ tested using DNA based or Phenotypic/biochemical based methods. The resulting fingerprint profile can be compared to an existing data base of faecal sources and matched to identify the source.                                                        

  Decision analysis trees are provided for suspected human faecal pollution, animal/bird faecal pollution, or mixed source faecal polllution

FAECAL framework human suspected

 Example of Decision Analysis Tree - Detection of human faecal pollution


The results from the methods outlined can be used to identify the species that was likely the cause of the faecal contaminant of the study waterway. This information can then be used to direct and inform management strategies and budgeting to contain or reduce the source of faecal inputs into waterways at the source rather that excess spending in an undirected mitigation approach.


State of Development Please Select

Development Contact

Elaine Moriaty

Main Developers

  • Institute of Environmental Science and Research (ESR)


Outcome Areas Environmental
Management Domains Freshwater
Subdomains Water Quality
Intended End Users
  • Regional Council Scientist
  • Researcher
Steady State or Dynamic Unknown
Level of Integration Environmental

Input & Output Data


Open/Closed Source Open Source
Licence Type No Licence

User Information

User Interface Please Select
Ease of Use Please Select
Use in Policy Process Review (Issue Identification), Do (Policy Implementation)

See Faecal Source Tracking webpage for methods toolbox with supporting information and publications.

Technical Considerations

Keywords Faecal pollution, water quality, source tracking

Envirolink Tools:

- Microbial Source Tracking (MST) Tools for Water Quality Monitoring

 Faecal Source Tracking - webpage:  http://www.waterquality.org.nz/home/faecal-source-tracking/

 ERS webpage: https://www.esr.cri.nz/home/about-esr/our-science-in-action/identify-the-source-of-faecal-contamination/

Key References

Elaine Moriarty and Brent Gilpin (2009): Faecal source tracking in the Avon River, Christchurch. Report No. R09/67. Prepared for Environment Canterbury by Institute of Environmental Science and Research Ltd.

Other ESR Publications on faecal source tracking

Associated Case Studies

Faecal Source Tracking - Avon River, Christchurch

This indicator provides possible links to other more harmful micro-organisms which can cause disease in humans.


Other Key Case Studies

Envirolink Funded Case Studies - Southland Trial, Lower Matai River, Northland, Marlborough