Bulletin #7115, Bacteria in Water Supplies Part 2: How to Disinfect Your Well

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By John M. Jemison, Jr., Extension water quality and soil specialist, University of Maine Cooperative Extension.
Reviewed and updated by Laura Wilson, Assistant Scientist, University of Maine Cooperative Extension.

For information about UMaine Extension programs and resources, visit extension.umaine.edu.
Find more of our publications and books at extension.umaine.edu/publications/.

Table of Contents


water running from a faucetBacteria are single-celled organisms found in soil, on our bodies, on leaf material, in lakes, rivers, and streams. While surface waters commonly have bacteria, most groundwater supplies do not. This is because the conditions that favor bacterial growth (food, oxygen, warm temperatures, and favorable pH) are not frequently found in groundwater. Yet, many wells still have bacteria.

Bacteria may carry diseases such as typhoid, dysentery, and cholera. In drinking water, these bacteria can cause serious health problems. For example, in Missouri, four people died and 243 people became ill from drinking water with a strain of Escherichia coli (Geldrelch et al., 1992).

The water you use for drinking and cooking must be free of pathogenic bacteria. Whether you will get sick after drinking water from contaminated sources depends on the strength of the bacterial strain, the strength and health of your body, and the number of bacteria in the water. Unlike most chemicals, one low-dose exposure to some bacteria can cause serious ill effects (Adamson et al., 1993). If you have bacterially contaminated water, you need to drink bottled water until you have properly disinfected the well.

State and federal governments require all public water supplies to be safe. However, you, as the homeowner, are responsible to ensure that your water supply is safe. Bacterial contamination is the most common water quality problem in Maine.

In Bulletin #7114, “Bacteria in Water Supplies, Part 1: Problem Bacteria and How to Test for Them,” we discussed how bacteria get into water supplies and water tests. In this fact sheet, we will discuss how to safely disinfect a well.

Disinfection Methods

If your water test results tell you that you have bacteria in your well water, you must not drink the water until it has been disinfected. One way to be sure drinking water is free from bacteria is to boil the water for five minutes. However, this does not really solve your problem. You still have a contaminated well. The bacteria in the well water, attached to the well casing, and in your plumbing also need to be killed. Treat your well, then do another water test. If bacterial problems come back after you treat the well, then you need to identify the source of the bacteria and try again. Contact your local University of Maine Cooperative Extension county office for information on keeping your well safe.

Whatever you do, you want as safe a process as possible, with as little damage to positive organisms, your plumbing or your health.

Most disinfection chemicals are toxic. Be careful when you use them.

The chemical you use for disinfection should be registered for use in Maine. As of 2011, there are 438 products registered for use in human drinking water as disinfectants (disinfectants are pesticides). Legally you are not permitted to apply a pesticide unless you have the specific label instructions. Often these label instructions are only available from the manufacturer as a supplemental label. Each disinfectant is different and you should obtain and use the correct label directions. For more information about pesticides labeled for use for drinking water disinfection in Maine, contact the Maine Board of Pesticides Control at 207.287.7545.

Attention homeowners with cold-water pressure tanks: Some tanks tend to harbor bacteria, once they are in the system. If you cannot get your water bacteria-free, you may want to replace the pressure tank.


Chlorination is probably the most common way people disinfect small public and private water supplies in Maine. It is an accepted standard method against which most other methods are compared.

Chlorine will also react with organic materials, breaking them down into simpler compounds. This is important to know because some of the chlorine you use to purify your water will get used up oxidizing material. This is called “the chlorine demand” of the water supply. It affects how much chlorine is left to attack bacteria cell walls. So, for chlorination to work, you need

  1. enough chlorine free to attack enzymes; and
  2. enough time for chlorine to work on the water.

If you have both, you’ll be able to kill the bacteria.

Chlorination Methods

Most private wells and water systems can be disinfected with one chlorine treatment. In most cases, if the well requires a chlorination system, either it is not structurally sound, or bacteria are getting in without filtration.

Shock chlorination involves a one-time, high-level chlorination process. It’s useful when you finish or repair a well or want to treat a contaminated well. See Table 1 for the steps required for shock chlorination.

Sometimes a continuous chlorination system is necessary—for instance, a continual problem with iron bacteria can be solved with a simple chlorination system. Simple chlorination systems keep a low level of chlorine in the water (0.2 to 0.5 milligrams per liter) for 30 minutes. Public water systems are required to maintain a 0.2 to 0.7 milligram-per-liter chlorine residual after a 10-minute contact time. Contact a water treatment professional for more information.


When chlorinating water supplies, you need to be careful that trihalomethanes (THMs) don’t form in the process. These chemicals form when free chlorine reacts with natural organic substances.

Methylene chloride, bromodichloromethane, and chloroform are examples of THMs. These chemicals are considered carcinogens. Several studies have shown that they may increase your risk of getting pancreatic, bladder or rectal cancers (Ijsselmuiden et al., 1992; Morris et al., 1992).

However, remember that

  1. there is very little organic material in groundwater;
  2. the potential for human exposure to THMs from drinking water varies with the season, contact time, water temperature, pH, and disinfection method; and
  3. the health risks from drinking contaminated, untreated water are higher than the risk of cancer from THMs.

If you shock-chlorinate and purge your well system, the chance of having any THMs is very low. On the other hand, if you take water from a lake or pond and super chlorinate the water, there is more organic material in the water and the potential for THM formation is higher.

Table 1: General Steps to Shock-Chlorinate a Well

  1. Buy enough bottled water to meet your needs for several days.
  2. Find out the depth and diameter of the well.
  3. For each 10 feet of six-inch diameter well, add four ounces of bleach. For an eight-inch diameter well, add seven ounces per 10 feet. There are 128 ounces in a gallon jug of bleach.
    For example: You have a 250-foot well that is six inches wide. Four ounces of bleach x 25 (25 10-foot intervals in a 250-foot well) = 100 ounces of bleach.
  4. Add the bleach to the well. Run a hose from the house to the well to start circulating water. Run water down the sides of the well casing with the hose to kill bacteria stuck to the sides of the well casing.
  5. If you have a hot-water tank, add eight ounces of bleach directly to it (to flush out bacteria).
  6. Turn on all water faucets, flush toilets and start washing machines, showers. This will bring bleach through lines and into the house. Once you smell bleach in all the faucets, turn the water off.
  7. Do not use the water. Let the bleach remain in the water lines for eight to ten hours or overnight.
  8. After eight to ten hours, drain the chlorinated water from the house through an outdoor spigot via a hose. If you do not have an outdoor spigot, attach the hose to the kitchen (or other) sink and run a hose out the window away from lakes, ponds and vegetation. Do not flush the chlorinated water through the septic leach lines. Direct the water down the driveway away from vegetation; bleach will kill grass. The chlorine will evaporate into the air.
  9. Wait at least a week after you can no longer smell the bleach, then retest for bacteria. If you test before the chlorine is out of the system, you will have an inaccurate test. Use the water regularly for wash and other activities, but use bottled water for drinking and cooking until you know the disinfection worked.

Note: Chlorine bleach, when used to disinfect well water, is a pesticide. In order to apply a pesticide in Maine, it is necessary to obtain and understand the label directions pertaining to the specific product use. There are many chlorine sources licensed in Maine for well water treatment. The University of Maine Cooperative Extension does not endorse any specific product. Contact the Maine Board of Pesticides Control at 207.287.2731 with any questions about pesticide licensing in Maine.


Adamson, R.H.”Waterborne Pathogens: Assessing Risk.” Health and Environment Digest 7 (1993):1–8.

Geldreich, E.E., et al. Water Research 8 (1992):1127-1137.

Ijsselmuiden, C.B., et al. “Cancer of the Pancreas and Drinking Water: A Population-Based Case-Control Study in Washington County, Maryland.” American Journal of Epidemiology. 136 (1992):836-842.

Information in this publication is provided purely for educational purposes. No responsibility is assumed for any problems associated with the use of products or services mentioned. No endorsement of products or companies is intended, nor is criticism of unnamed products or companies implied.

© 2002, 2011

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