This page has been archived on the Web

Information identified as archived is provided for reference, research or recordkeeping purposes. It is not subject to the Government of Canada Web Standards and has not been altered or updated since it was archived. Please contact us to request a format other than those available.

Skip booklet index and go to page content

Microbial Source Tracking in Aquatic Ecosystems: The State of the Science and an Assessment of Needs

Microbial Source Tracking Needs Assessment

Fecal contamination of aquatic ecosystems has resulted in adverse public health and economic consequences for many communities across Canada. This fecal contamination can originate from many possible sources, although municipal effluents, agricultural practices and wildlife populations represent the more common sources in many areas across Canada.

Municipal Effluents

Communities need to be able to track sources of municipal wastewater, combined sewer overflows and stormwater contamination quickly because of the relatively higher potential for the occurrence of waterborne pathogens of human health concern. This fecal pollution can come from inadequately treated effluents from sewage treatment plants, or sewage treatment plant bypasses, and from stormwater and combined sewer overflows. Leaking septic tanks, and shipboard wastes or "grey water" can be other sources of human fecal contamination in aquatic ecosystems. One complication for microbial source tracking is that municipal wastewater may not contain microbial contaminants exclusively of human origin. Municipal wastewater can also contain fecal contamination from food processing activities, and from urban runoff sources like pets and urban wildlife.

Dr. Jiri Marsalek, National Water Research Institute, Environment Canada, Burlington, Ontario, provided a presentation on fecal pollution challenges in urban environments. Fecal contamination occurs frequently in urban waters as a result of discharges of various municipal effluents, among which wet-weather flows, stormwater and combined sewer overflows (CSOs) are particularly important. Both stormwater and CSO discharges can be highly contaminated with fecal bacteria and widely distributed throughout urban areas. As such, they need to be addressed in planning the protection of recreational waters. Stormwater characterization data indicate concentrations of E. coli or fecal coliforms in the range from 103 to 105 units per 100 mL. Such concentrations may be attenuated prior to discharge into open waters by stormwater management measures, or exceptionally by disinfection. The levels of indicator bacteria in CSOs are much higher than in stormwater, and can be as high as 10 6 E. coli per 100 mL. Consequently, the abatement of fecal contamination of CSOs is now considered in the design of CSO control and treatment, as stipulated in the Ontario Interim Directive F-5-5 for CSO abatement. In some cases (e.g., the Toronto Waterfront), the abatement of fecal contamination of receiving waters is among the primary drivers behind the often costly CSO abatement programs. CSO abatement options comprise combinations of storage and treatment, in which the CSO treatment train generally includes disinfection, particularly where CSO outfalls are located upstream of recreational waters. Indicator bacteria data from studies in the Upper Great Lakes Connecting Channels (Ontario) were used to demonstrate fecal contamination impacts of wet-weather flows.


While it is possible to treat livestock fecal wastes effectively, and apply manure to agricultural lands safely, poor farming practices, or storms and surface water runoff can result in fluxes of fecal pollution downstream into aquatic ecosystems. Communities need to be able to track sources of livestock fecal pollution quickly to prevent contamination of source waters used for drinking water, irrigation or recreation. Increasingly intensive rearing practices for livestock animals like cattle, hogs and poultry will present significant animal waste management challenges in the future. Management of aquatic ecosystems in agricultural watersheds will need to consider potential livestock fecal pollution sources (e.g., droppings on pastures, manure lagoons) and the timing of events like manure spreading when investigating potential fecal pollution sources.

Cattle in a stream add to fecal contamination of the water | Photo: Tom EdgeKatrin Nagelschmitz, Strategic Policy Branch, Agriculture and Agri-Food Canada, provided a presentation outlining the diversity and numbers of livestock in agricultural areas across Canada. Livestock numbers have increased in Canada over the last decades. However, the impact of this trend differs across the country. The change in livestock densities and in manure production varies among regions. Technological and structural changes in the livestock sector are causes of the development. The trend is towards specialized larger farms employing a smaller immediate land base.


Wildlife can present an unpredictable and difficult fecal source tracking challenge, that is not so amenable to control and familiar waste treatment practices. Notable are the growing numbers of birds such as gulls and Canada geese in many areas across Canada. Where aquatic ecosystems occur near large wildlife populations (e.g., bird colonies), consideration needs to be given to monitoring wildlife populations, their fecal droppings, and their seasonal migrations or behaviour characteristics that could contribute to fecal contamination.

Dr. Tom Edge, National Water Research Institute, Environment Canada, Burlington, Ontario, provided a substitute presentation on wildlife fecal contamination sources. Fecal pollution from wildlife species has been shown to contribute to impairment of recreational waters in areas across Canada. For example, fecal droppings from birds along beaches or from birds roosting under bridges can lead to significant increases in waterborne fecal indicator bacteria. In some areas, efforts to enhance biodiversity habitat and establish buffer strips along streams may also facilitate increased loadings of fecal pollution from wildlife. MST studies need to evaluate wildlife species as possible sources of fecal pollution, and to consider the significance of local wildlife populations such as aquatic mammals or birds (e.g., gulls and geese), and the timing of wildlife movements and migrations.

Date modified: