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Water Safety : Pathogens and Your Well Water

What’s in your well’s water, besides water?

Only test results that are carried out by an accredited laboratory can tell you for sure.

When you submit your well water to an accredited laboratory for testing, it will be analyzed for the presence of indicator organisms (e.g. Total coliforms and E. coli). These organisms are indications of contamination, in the well or the water distribution system or could have been introduced at the point of sampling.

These indicator organisms serve as an alert of contamination which could include pathogens which are organisms that can make people sick. When it comes to well water, pathogens of concern include certain forms of bacteria, protozoa and viruses. While each of these organisms can lead to different illnesses of varying severity, there are some very unpleasant symptoms common to many, including diarrhea, nausea, abdominal cramps and low-grade fevers.

Your well is your first line of defence against harmful organisms reaching your water supply. Maintain your well regularly and thoroughly. It’s easier to prevent problems than to fix them. To complete your well water safety routine, get your water tested regularly.

Three uninvited guests: bacteria, protozoa, and viruses

Bacteria are a natural part of life. In fact, there are many forms and functions of bacteria we couldn’t live without, such as those that break down organic matter like food waste and leaves.

Water is a preferred environment for bacteria because their membranes could otherwise dry out. But some bacteria in water can lead to serious illness or disease, such as gastroenteritis or salmonellosis. These days, E. coli O157:H7 is probably the most infamous disease-causing bacteria.

Some protozoa can live in animals and humans, and are passed in feces. These tiny parasites are able to survive in surface water for long periods of time as dormant cysts. Some waterborne protozoa can cause illness, such as giardiasis (beaver fever) or cryptosporidiosis.

Viruses reproduce by infecting living cells. Some viruses found in water cause illness, including Hepatitis A and the Norovirus (Norwalk-like virus).

Protozoa and viruses are usually found only in surface water that has been contaminated by animal or human feces. However, ground water can become contaminated through contact with surface water. In other words, if surface water can penetrate any unsealed joint or crack anywhere in your well, your water is at risk.

More about E. coli

The most harmful pathogen is Escherichia coli (or E. coli) O157:H7. It spreads through water and contaminated food like undercooked hamburger. Symptoms may include stomach cramps, vomiting, fever and diarrhea. Severe cases can progress to kidney failure in the elderly and children. Early symptoms are common to a number of diseases, and may or may not be the result of contaminated drinking water. Talk with your doctor for more information about E. coli.

Although E. coli O157:H7 can cause serious illness, most of the other hundreds of E. coli strains are harmless, and some are even beneficial. In fact, E. coli make up part of the natural flora - These are the bacteria that live in your large intestines.

How pathogens move through and survive in soil

As described in Get Acquainted with Your Well, when surface water travels down through soil to ground water, it can take harmful pathogens with it.

Fortunately, soils can have a cleansing effect on harmful pathogens. But if they are able to bypass soils’ natural cleansing action, pathogens can survive. Bypass routes can introduce human and animal wastes into ground water by reducing the time and distance it takes to travel through soils. The shorter the travel time, the greater the risk of contamination.

Have you built an expressway for pathogens?

Some of the facilities or activities on your property might be providing pathogens with these bypass routes. A well that is poorly constructed or plugged provides one route. An on-site septic system that is improperly or poorly designed, maintained or located provides another route.

Weather can also create a bypass route. Very heavy rains or flooding can move contaminants through soil at faster rates than normal.

Diagram showing the flow of pathogens

The arrows show the pathways that pathogens can follow to get into an improperly constructed, shallow well. The red shading indicates the annular space, which is the space outside the well casing that was created when the hole for the well was made. In this well, the annular space is unsealed at the top, and acts as a duct for contaminated surface water to pass down into the well intake at the bottom. To make matters worse, contaminated surface water can also enter the well through unsealed tile joints and cracks. For more information about well construction and maintenance see the Fact Sheet,  Get Acquainted with Your Well.

Is your well playing host?

Get in the habit of putting your well water to the test

How do you know if your well water is playing host to unwanted organisms? Regular testing of your well water is the best way.

Test your well water regularly. Three times per year – spring, summer and fall – is recommended. Routine testing also provides an early warning signal of potential problems.

Some water-testing vocabulary

When drinking water is tested for biological (as opposed to chemical) contamination, the bacteria are called indicator organisms or indicator bacteria. If the test results indicates that there is no significant evidence of bacterial contamination, it does not mean that the water does not contain other contaminants such as chemicals.

The presence of these biological indicators acts as an early warning signal. They tell you that there are health risks with your well water. The indicator bacteria usually show up in a test if your water has become contaminated with surface water or sewage.

There are two indicator organisms that public health labs will test for when you submit a sample. These are Total coliform and E. coli.

Total coliform

  • are a general family of bacteria that is found in animal wastes, surface soils and vegetation
  • indicate contamination of water with organisms, and possible evidence of surface water contamination in your well water
  • provide an early warning signal that there may be a problem with your water supply

E. coli

  • are a group of bacteria that live in the intestines of warm-blooded animals
  • indicate recent fecal contamination from sources such as human sewage or livestock waste
  • indicate that there is a problem with your water supply

Don't use water that has tested positive for a significant amount of Total coliform or any E. coli. Don't use it for drinking, making infant formula and juices, cooking, making ice, washing fruits or vegetables, brushing teeth, bathing or showering. And unless you've disinfected it, don't use it to your wash hands.

If your test results show the presence of indicator organisms, take action! Everyone who drinks from your well is at risk. You must identify the source of contamination and prevent its access to your well. It’s important to get the job done quickly and right; consult a well contractor or your local public health unit as soon as possible.

If your results show that your drinking water contains no significant evidence of bacterial contamination, then continue to have the water tested at least three times per year. One of the three samples you send for testing should be taken in the spring.

Sample your well water until you have three consecutive samples (collected one to three weeks apart) with less than 5 Total coliform and no E. coli.

Changes in your water

It’s important to know the difference between water quality that could relate to health concerns (or health parameters) and those processes in nature that only affect the appearance, smell or taste of your water (or aesthetic parameters).

A change in your water’s aesthetic parameters is not necessarily a health risk. However, they might signal contamination or deteriorating water quality. If you notice a change in these parameters, you should submit a water sample for testing as soon as possible.

If you are concerned about the potential presence of a particular contaminant, make sure the contaminant is specifically tested for.

To learn more about what’s involved in having your well water tested, refer to Putting Your Well Water to the Test.

For more information about long-term water treatment options refer to Choosing a Water Treatment System.

Test three times annually, and when...

In addition to regular testing, well water should be tested :

  • after any repairs such as a pump repair or replacement
  • if the well has not been used for several weeks
  • if there has been flooding in the area, or
  • there has been a change in water appearance, colour or odour.

And if you have one of the highly vulnerable water supplies described in Get Acquainted with Your Well, you may want to test your well water more frequently.

See also :


For more information
Call the ministry INFOline at 1-866-532-3161
(Toll-free in Ontario only)
TTY 1-800-387-5559
Hours of operation : 8:30am - 5:00pm
Ministry of the Environment
Information Centre : 1-800-565-4923
Water Well Records : 1-888-396-9355

Ministry of Agriculture and Food
OMAF Agricultural Information Contact Centre :
1-877-424-1300

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