Bacteria, microscopic in size, are the smallest single-celled organisms that can live completely on their own because they have the ability to ingest food and transform it into energy. The vast majority of bacteria found in water do not cause disease; however, some can. These are called pathogens. Bacteria are important residents of groundwater, transforming organic carbon, forms of common elements and minerals such as iron, manganese, sulfur, phosphorus, nitrogen and oxygen.

An unknown but very large number of bacterial types make their homes in groundwater. Many were deposited with the aquifer’s formation material and others enter groundwater from recharge. Bacteria in groundwater are mostly engaged in transforming minerals to obtain energy, and sometimes affect the operation of wells. Coliform bacteria are bacteria that are naturally present in the environment, breaking down organic carbon. For over a century, they have been used as an indicator that other, potentially harmful, bacteria may be present. Fecal coliform and Escherichia coli (E. coli) are a portion of the total coliform bacteria group whose presence indicates that water may be contaminated by human or animal wastes and harmful to human health. Some strains of E. coli are pathogens.

The vast majority of the bacteria found in groundwater (often in numbers > 104 cells per cubic meter) are native residents of the aquifer, ancestors laid down with the aquifer material, or moving through with recharge. These bacteria naturally enter a well when water is pumped. Some settle on well and well equipment surfaces.

Potential sources or pathways of bacteria that may be of health concern include:

  • Runoff from woodlands, pastures, and feedlots; septic tanks and sewage plants; and animals (wild or domestic).
  • Backflow from contaminated sources such as a sink-top carbon filter or bucket of water.
  • Reduced pressure or suction in water lines that draws in soil water at the pipe joints.
  • Through faulty sanitary seals in the well system such as when the well cap, grout around the well casing, or pitless adapter that connects an underground water distribution pipe to the well are compromised.

While the vast majority of bacteria in groundwater are not pathogens, some bacteria, mostly originating with humans and their livestock, are of interest in public health for both animals and people. Among these, most coliforms are not pathogens, but they serve as indicators of the microbial quality of water. An indicator is easily cultured, often present when pathogens are present, but in far greater numbers than the pathogen. Pathogens—the bacteria, protozoa, and viruses that make people sick—can be rare and difficult to detect even if they are present in the water. Total coliforms are indicators and are more common and easy to grow. Testing for them provides a margin of safety.

Pathogens may not be present if coliforms are, but some strains of E. coli (a species in the total coliform group) have been lethal, so their presence should be taken very seriously. Other health effects from pathogenic bacteria can include diarrhea, cramps, nausea, headaches, or other symptoms. They may pose a special health risk for infants, young children, and people with severely compromised immune systems. Even without pathogens present, large numbers of coliform bacteria indicate connection with soil and poorly filtered water, and possibly breaks in sanitary seals protecting water systems.

People become accustomed to the natural bacteria in their water while guests may experience some discomfort or diarrhea.

Bacteria that cause biological fouling of water systems typically do not cause disease themselves, although some, such as species and strains of Pseudomonas, can cause infections and pneumonia. However, they can harbor coliform bacteria and pathogens, impair well and water system function, and cause unsightly discoloration that is an indicator that well and water system cleaning should be performed.

The best way to assess your well system’s risk for bacteria is to 1) test the water annually for bacteria, typically a total coliform test, although others are available, and 2) to periodically get an inspection to make sure there are no maintenance problems that might allow bacteria to infiltrate the well system.

Well inspections should be done by a qualified water well system professional and include visual inspection of the wellhead, the surrounding area that may include sources of undesirable bacteria, well system components, and other related equipment; physical inspection of well system components; a pumping test with water quality samples collected, and documentation of the entire inspection. An option is a downhole or borehole video inspection, which provides a direct view of the well, usually with the pump removed. This inspection is usually reserved for situations where a problem is suspected.

Several measurements are used depending on the situation. In general total heterotrophic plate count (HPC), a rough measure of total viable (living, can reproduce) bacteria, is expressed as cell forming units (CFU) per milliliter (mL) (CFU/mL). Total coliform bacteria and E. coli results are often expressed as CFU/100 mL. These latter bacteria are often now measured using liquid tests, and a very common result will simply be “present” or “absent.”

Standards and goals: The U.S. Environmental Protection Agency Maximum Contaminant Level Goal for total coliform bacteria, fecal coliforms, and E. coli is zero. That is, a presence-absence (P/A) test should be “absent”. However, many jurisdictions recognize that total coliform bacteria are natural residents, and may set a low standard such as 4 CFU/100 mL for TC, while E. coli must be 0 (<1) CFU/mL. Some purposes such as bottled water or laboratory water may set a standard for HPC.

Measurements for biofouling, natural residents, and genetic testing are subject for another article.

Treatment methods include:

  • Disinfection, which kills the bacteria (i.e. chlorination or disinfection via ozone or bromine)
  • Filtration, which traps the bacteria
  • Percolation which removes and can kill the bacteria
  • Ultraviolet irradiation, which kills bacteria and degrade viruses.

Sometimes conditions may dictate using a combination of methods to effectively deal with bacterial contamination of well water. All of these methods require proper maintenance by a qualified professional.

Cleaning and disinfection of the well is often a necessary step that removes biomass, places for undesirable bacteria to hide, and sources of damage to water system components. Well cleaning and disinfection reduces pressure on and maintenance impacts on water treatment systems.

In addition to the information on, you can call the toll-free Private Well Owner Hotline at 855-420-9355 or visit the National Ground Water Association Website, You can learn more about appropriate treatment technologies for bacteria by visiting the Websites of two organizations that certify home drinking water treatment systems: The National Sanitation Foundation at and the Water Quality Association at You should also know about the services and resources available from your local and state health protection agencies or offices.

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