6.3 Vulnerability to Contamination

Domestic wells can be vulnerable to contamination because they are often located close contaminant sources, and they often draw water from shallow, unconfined aquifers that are susceptible to contamination from human activities on the land surface. Many domestic well owners do not maintain their well or check the condition of their well regularly. The lack of well maintenance can result in unsanitary conditions and poor water quality, as shown in the examples in Figure 15.

Photos showing examples of unsanitary conditions at domestic wellheads

Figure 15  Examples of unsanitary conditions at domestic wellheads; a) cobwebs inside a well indicating insect activity; b) dead rodents floating in a well; c) dug well with abundant roots protruding though the brick-lined walls; and, d) flooded well pit and missing well cap allowing surface water to enter the well (photographs by Stew Hamilton).

Contaminant Sources Near Domestic Wells

Domestic wells are often located close to contaminant sources, such as a septic system, a heating oil tank (Figure 16), a farmyard, or a road where salt is applied for de-icing during the winter. Household pets are another potential source of contamination, from either pet feces near the well or the burial of deceased pets on the property. The population of cats and dogs in Canada in 2020 was estimated to be about 16 million (CAHI, 2021), equal to about 42 percent of the human population. The proximity of these multiple types of contaminant sources to domestic wells makes the wells vulnerable to contamination. Unlike many municipal wellfields, domestic wells do not have wellhead and wellfield protection plans in place to manage the risks that these contaminants pose.

Photo showing two domestic wells located near a home heating oil tank

Figure 16  Two domestic wells located near a home heating oil tank. This example shows how domestic wells can be subject to multiple vulnerabilities, including droughts and contaminant sources. The dug well (left foreground) has been replaced with a deep drilled well (right, with a blue well cap) because seasonal droughts frequently caused this shallow dug well to go dry. Both wells are located close to a heating oil tank (grey tank beside house), which could contaminate the wells if an oil leak or spill occurred (photograph by John Drage).

In rural areas there is often no central public water supply or central wastewater system available and, therefore, a homeowner will have both a domestic well and a septic system located on their property (Figure 17). Although most well construction regulations specify a minimum separation distance between wells and septic systems (typically ranging from 15 to 30 m), they are usually located relatively close to each other because they must both be located on the homeowner’s property and close to the house. In subdivisions, there can be multiple septic systems present and, therefore, even if a well owner installs their well upgradient from their own septic system, it may be down-gradient of their neighbor’s septic system.

Figure showing a household with a domestic well and septic system

Figure 17  A household with a domestic well and septic system, showing the potential for septic system effluent to flow towards the well (modified from Waller, 1994).

A properly functioning septic system can reduce contaminant concentrations so they do not adversely impact water wells, provided that both the septic system and well are properly located, designed, constructed, and maintained. Nonetheless, rapid contaminant transport can occur in certain conditions. A study that examined 248 disease outbreaks (23,000 illness cases) associated with untreated groundwater, including public groundwater systems and domestic wells, found that human sewage was the most common source of contamination (Wallender et al., 2014). The study also concluded that for the majority of cases (67 percent) where the contributing factors were known, the contamination was facilitated by improper design, maintenance, or location of septic systems or water wells. Further information about septic system impacts on groundwater quality can be found in another book in the Groundwater Project series (Robertson, 2021).

In addition to the common sources of contaminants located on a homeowner’s own property, domestic wells are sometimes located close to commercial, industrial, or agricultural contaminant sources. For example, gas stations, dry cleaners, landfills, and crop fertilizing activities are known to have caused domestic well contamination. Box 3 discusses an example of a domestic well that has been contaminated by activities carried out at a waste disposal site.

Domestic Wells in Shallow Aquifers

Domestic wells are inherently more vulnerable to contamination from human activities because they often draw water from shallow aquifers that are susceptible to contamination from human activities on the ground surface. Domestic wells tend to be shallow for economic reasons. Homeowners must pay for their well construction and, to keep costs low, they will usually stop drilling as soon as the well is deep enough to provide enough water to meet their needs. A study in the US that looked at over 1,200 wells of various well types from across the country reported that the median domestic well depth was 49 m, compared to 130 m for public wells (DeSimone et al., 2009).

As indicated in Figure 18, the travel time for contaminants to migrate from the ground surface to the intake of a shallow well may be days to years. This provides limited opportunity for contaminants to be attenuated before they reach the well. In contrast, deeper public water supply wells may have groundwater travel times ranging from years to centuries. The longer the groundwater travel time, the more opportunity there is for the concentrations of anthropogenic contaminants that originate at the ground surface to be reduced by natural attenuation. A deep well is also more likely to be protected from contamination by confining layers located above the well intake zone.

Figure showing groundwater and contaminant travel times

Figure 18  Groundwater and contaminant travel times for shallow domestic wells are shorter than for deeper public wells, providing less time for anthropogenic contaminants to be attenuated (modified from Dubrovsky et al., 2010).

Microbial Contaminants in Domestic Wells

As discussed in Section 5, Water Quality of Domestic Wells, microbial contaminants are among the most common type of contaminants found in domestic wells. Regional surveys of domestic wells (Table 2) often detect bacteria in about one third of sampled wells. Microbial contaminants are found in all types of wells, not just domestic wells, but they are detected more frequently in domestic wells than public wells. For example, a national survey of microbial water quality in the United States tested 405 domestic wells and 227 public wells and reported that coliform bacteria were detected in untreated water in 33 percent of domestic wells and 16 percent of public wells (Embrey and Runkle, 2006). A review of waterborne infectious disease outbreaks in England and Wales reported that private water supplies, most of which are sourced from domestic wells serving individual households, had incidences of outbreaks up to 35 times more than public water supplies (Smith et al., 2006).

Why are domestic wells more vulnerable to microbial contamination? There are many factors that control the risk of microbial contamination in wells, including the characteristics of the microbial sources near the well (e.g., proximity of the source, quality of construction and maintenance of nearby septic systems) and the migration pathways that allow microbial contaminants to travel from the source to the well. Migration pathways include both hydrogeological pathways and pathways associated with the well’s construction. Figure 19 shows examples of common conditions that can cause microbial contamination in domestic wells.

Figure showing examples of common conditions that can cause microbial contamination in domestic wells

Figure 19  Examples of common conditions that can cause microbial contamination in domestic wells.

Studies that look at the causes of microbial contamination in domestic wells usually investigate correlations between well contamination and the well characteristics, including its proximity to contaminant sources, its hydrogeologic setting, and its construction. With respect to contaminant sources, septic systems, feedlots, and manure spreading have been associated with microbial contamination. A report that pooled data from 55 studies on pathogen contamination in groundwater systems found that septic systems were the most frequently confirmed or likely source of contamination (Hynds et al., 2013). A study in Florida, USA, found that decreasing distance between domestic wells and septic tanks was correlated with increasing concentrations of fecal coliform bacteria in wells (Arnade, 1999). Studies of domestic wells in agricultural areas have found that wells located closer to animal feedlots and manure spreading activities have a higher risk of bacterial contamination (Goss et al., 1998; Conboy and Goss, 2000).

With respect to hydrogeological settings, several studies have reported that microbial contamination is more common in wells constructed in fractured rock and carbonate rock, compared to wells in unconsolidated aquifers (Lee and Murphy, 2020; DeSimone et al., 2009; Embrey and Runkle, 2006; Kraus and Griebler, 2011). This can be attributed to the lack of natural attenuation of microorganisms and the rapid contaminant transport that can occur in fractures and karst solution channels. A study in New Jersey, USA that analyzed data from 51,000 domestic wells found that bedrock wells were three times more likely to have coliform bacteria present compared to wells in unconsolidated aquifers (Atherholt et al., 2013). The same study reported that bacteria was more frequently detected in wells in areas with thin till layers (< 6 m) overlying the bedrock, than wells with thick till layers (6 to 60 m). Bedrock aquifers with thin overlying soil profiles are more vulnerable to microbial contamination because there is less opportunity for contaminants to be removed by natural attenuation as water percolates through the soil.

Well construction is frequently cited as a cause of microbial contamination in well water. A review of 55 studies of pathogen contamination in groundwater supplies in Canada and the United States reported that there are 50 percent more cases of pathogens in poorly designed and constructed wells than adequately designed wells (Hynds et al., 2014). Well construction factors that are commonly associated with microbial contamination in domestic wells include shallow well depths (or shallow intake zones), dug wells, and older wells (Owusu et al., 2021; Lee and Murphy, 2020; Goss et al., 1998). Shallow wells access shallow groundwater with relatively short travel times that have less opportunity to attenuate microorganisms. It is important to note that it is the minimum depth of the water intake zone that controls whether shallow groundwater enters a well, not the total depth of the well. For example, a well that is 50 m deep with 6 m of casing and annular seal can allow shallow groundwater from a depth of 6 m to enter the well.

Dug wells are more susceptible to microbial contamination because they are shallow and often the casing and/or annular seals are not continuous. Older wells can be susceptible to microbial contamination because they may have deteriorated over time (e.g., cracks or holes have developed in the casing, or annular seals have failed) or may have been installed using outdated well construction methods. Common well integrity problems that can cause microbial contamination include poor surface seals at the wellhead (allowing surface water to enter the well), no sanitary well cap (allowing vermin to enter the well), and inadequate, or failed, casing and annular seals. With respect to annular well seals, researchers have observed that cracks and voids in grout can develop over time and dye tests have shown that these grout failures can allow dye to migrate to significant depths (> 10 m) below the ground surface (Olafsen Lackey et al., 2009).

Risk factors commonly associated with microbial contamination are summarized in Table 3. In general, wells have a higher risk of microbial contamination if:

  • they are located near a microbial source (e.g., septic system, animal feedlots, manure spreading);
  • they are located in a hydrogeological setting that allows for rapid microbial transport (e.g., fractured rock, carbonate rock, areas with thin soil profiles); and/or,
  • they have well construction characteristics or deficiencies that make them susceptible to microbial contamination (e.g., shallow intake depths, inadequate casing and grout, poor sanitary wellhead conditions).

Table 3  Examples of sources and pathways that can cause microbial contamination in well water.

Sources & Pathways

Risk Factors



Septic systems

Septic systems that have failed, or are too close to water wells, may cause contamination.

Animal feedlots

Wells close to feedlots are reported to have a higher risk of bacterial contamination.

Manure spreading

Manure spreading near wells has been reported to increase the risk of bacterial contamination.


Fractured rock

Fractured rock provides less natural attenuation than unconsolidated aquifers and can have fast groundwater velocities that lead to rapid microbial transport.

Carbonate rock

Carbonate rock can have fractures and karst solution channels with rapid microbial transport and minimal natural attenuation.

Thin unconsolidated materials

Thin soil and sediment layers provide less attenuation of microorganisms than thick layers of unconsolidated materials.

Shallow water tables

Shallow water tables or thin unsaturated zones provide less opportunity for attenuation of microorganisms.

well construction

Shallow wells

Shallow groundwater has shorter travel times to reach the well and less opportunity for attenuation of microorganisms.

Dug and bored wells

These wells are shallow and often lack continuous casing and annular seals.

Older wells

Older wells may have deteriorated casing and annular seals and may not be constructed to modern standards.

Poor annular seals

Inadequate or failed annular seals can allow shallow water to enter the well.

Inadequate casing

Inadequate or deteriorated casing can allow shallow water to enter the well.

Poor surface seal at wellhead

Poor surface seals, that do not slope away from the well and do not provide low permeability seals at the ground surface, can allow surface water to enter the well.

No sanitary well cap

Sanitary well caps prevent vermin from entering the well.

Some of these factors, especially the hydrogeologic setting, are not specific to domestic wells but can affect all well types. However, as noted earlier, domestic wells are more susceptible to microbial contamination than public water wells because they are more likely to be shallow, located near a microbial source, and have well construction deficiencies.

Because there are multiple risk factors that can cause microbial contamination in wells, public water supplies commonly use a multi-barrier approach to reduce risks. Macler and Merkle (2000) explain that the multi-barrier approach for groundwater supplies typically includes:

  • source water protection (i.e., controlling the sources of contamination in the well’s capture zone);
  • wellhead integrity monitoring and maintenance (i.e., controlling migration pathways at the well);
  • water treatment (i.e., water disinfection to remove pathogens); and,
  • water quality monitoring.

Most jurisdictions recommend these multi-barrier practices to domestic well owners, including source protection (i.e., maintaining septic systems, setback distances between wells and septic systems), routine well inspection and maintenance, and routine water quality testing. Water disinfection is clearly associated with reduced microbial contamination in public water supplies, and it would be prudent to include disinfection as a standard practice for domestic wells. Water disinfection systems, such as ultraviolet lights, are effective, simple to operate and maintain, and are relatively inexpensive compared to the construction cost of a domestic water well.


Domestic Wells – Introduction and Overview Copyright © 2022 by John Drage. All Rights Reserved.