What to Do if Your Drinking Water is Contaminated with Bacteria

Drinking water contaminated with fecal coliform, or E.coli, bacteria can cause health problems.

  1. Boil for one minute all water to be used for drinking, cooking, washing fruits and vegetables, brushing teeth, and making ice cubes, baby formula and concentrated juices.

  2. Look at the location and construction of your well to find the source of contamination and then fix it.

  •  Wells and springs should be isolated, preferably uphill from septic systems and other potential contamination sources, such as barnyards and pastures.

  •  Dug wells and springs should be made of concrete and have tight-fitting, lipped covers and sealed joints. Drilled wells should have casings that extend 18 inches above the ground, surrounded by mounded clay to prevent surface water from entering.

Learn more about drilled wells, dug wells and springs

How to Disinfect Your Water System

Before you disinfect your well

1. Visually inspect your well and water system and make any repairs.

2. Test for nitrate and chloride.

  • A septic system or nearby farm could be the source of contamination.

3. Draw enough water to last for 3 to 5 days.

  • If you have bacteria in your water, boil for one minute any water used for drinking, cooking, washing food, brushing teeth, or making ice or baby formula. You can also get or buy water from another safe source.

4. Flush your well.

  • Turn on an outside spigot and flush at least three times the total volume of the well. Be careful not to pump the well dry, which could damage it.

  • Do not drain the water into your septic system since it could overload it.

  • Test your water for bacteria again since flushing can sometimes get rid of it.

Step-by-step guide to disinfecting your well

Download or print the step-by-step disinfection guide

You will be adding chlorine bleach directly to your well. Chlorinated water will then travel throughout the plumbing and faucets in your home.

  1. Disconnect or bypass any water treatment devices, like water softeners or reverse osmosis units, since bleach can damage them. You will need to disinfect these devices separately according to the manufacturer’s instructions.

  2. Gather materials needed: rubber gloves, eye protection, household chlorine bleach that contains no scents or additives, 5-gallon bucket, small brush, garden hose, and a measuring cup. Wear rubber gloves and eye protection whenever you are working with bleach.

  3. Keep children and pets away from the area, especially from bleach and chlorinated water. Turn off power to the pump.

  4. Remove the well cap. Inspect and fix any exposed wires. You can turn power to the pump back on, but do not get the wires wet.

  5. Mix 1 cup of bleach with a half-gallon of water in the bucket. Use this water to clean the well cap and sides of a dug well using the scrub brush. Discard the water away from your septic system and any streams.

  6. Calculate the amount of bleach needed by using the chlorine calculator. Carefully pour the bleach into the well.

  7. Use the garden hose to run water into the well to mix and circulate the bleach. Run the water along the well casing or sides of the dug well. Do this for at least 15 minutes and up to 1 hour.

  8. Put the well cap back on. Install a new gasket if it is brittle or missing.

  9. Go to the faucet inside your home that is farthest from the well and run the cold water until you smell bleach. Turn the tap off, then do the same with the hot water. Repeat this step for all faucets, shower and baths, toilets, and outside spigots.

  10. Check the manufacturer's instructions before running the chlorinated water into your clothes washer, dishwasher or refrigerator water filtration system.

  11. Leave the chlorinated water in the plumbing for at least eight hours to give the chlorine time to disinfect your system.

  12. Flush the system until you no longer smell bleach. Start with an outside spigot. Connect a garden hose so it drains onto a gravel driveway or brushy area away from your septic system and any streams. You may want to run the water at less than full flow or turn the tap off periodically to allow the well to recharge so it does not run dry.

  13. Flush the taps inside your home by using a hose or bucket and drain the water outside the same way as in Step 15. Run the hot and cold faucets until you no longer smell bleach.

  14. Remove, clean, then replace any screens on your faucets as they can become clogged by debris dislodged during the disinfection process.

  15. Retest your water two to three days after the chlorine smell is gone. Order the bacteria test (Kit NU) from the Health Department Lab.

  16. Continue to either boil your water or get it from a safe source until no bacteria is detected.

If problems continue

The well casing may also need a thorough scrubbing or cleaning to remove bacteria that can build up on the well casing and borehole walls. Consider getting the well professionally inspected by a well contractor. They have the equipment to clean the well or run a camera down to find cracks or other issues. This is generally recommended every ten years.

Consider permanent treatment for your water supply if you have disinfected several times and a well inspection does not find the cause of the contamination. Make sure any treatment device is certified by NSF or ANSI.

Permanent treatment options include:

  • Ultraviolet (UV) light treatment that meets NSF/ANSI Standard 55

  • A filter that meets NSF/ANSI Standard 53 and is 1 micron (absolute), which is approved to remove disease-causing bacteria

  • A chlorinator, which injects exact amounts of chlorine into your plumbing system when the water is being pumped to the home.

Learn more about water treatment

How to calculate the amount of chlorine needed to disinfect a well

Using the Chlorine Concentration Calculator, enter in the:

  1. Depth of your well

  2. Depth to the water table

  3. Diameter of your well

Be sure to check the concentration of the bleach you use. The calculator will give you the amount of chlorine to use for 6% and 8.25% solutions. Many household bleach products are concentrated at 8.25%. Remember to use ordinary household bleach without any added chemicals.

Use the Chlorine Concentration Calculator

Watch this video to learn how to shock chlorinate your well. The video will help you understand your well water system, how to calculate the volume of bleach needed for disinfection, and how to safely apply it.

Your Questions Answered
My water is contaminated. Why hasn’t it made me sick?

Coliform or other bacteria will not necessarily make you sick. However, since these organisms have been able to enter your water system other disease-causing organisms (bacteria, viruses and protozoa) could enter as well. To prevent sickness, the Health Department recommends that you boil your water for one minute before drinking.

Can water tests pinpoint the exact source of contamination?

No. Water tests show that coliform bacteria have entered your water system, either at the source or between the source and the faucet. The tests can't tell you where the source of the contamination is.

I disinfected my well and consulted with the Health Department, but my water is still contaminated. What should I do now?

You may need to hire an environmental engineer or hydrogeologist to find the problem. The Health Department can give you a list of water system consultants and water treatment options. Call the Drinking Water Program at 802-863-7220 or 800-439-8550 (toll-free in Vermont) or email AHS.VDHEnvHealth@Vermont.gov.

Emergency Disinfection

To make water from a spring or well of unknown quality safe to drink on a temporary basis, follow the steps below. This method will protect against most, but not all, disease-causing organisms. (NOTE: These directions do not apply for disinfection of newly constructed, repaired, or bacteria-contaminated springs and wells. See “How to Disinfect Your Water System” above).

Steps for emergency disinfection
  • Mix the water with liquid chlorine bleach as shown in the Table of Chlorine Dosages below.

  • Mix the water and chlorine thoroughly and then let it stand for 2 to 3 hours. Store the water in a human-made covered reservoir, tank or other sealed clean container to protect against recontamination.

  • Spring, pond, stream or well water that is turbid (cloudy or containing particles) must be boiled for five minutes before using it for drinking, washing fruits or vegetables, and making ice, juice or baby formula.

  • Chlorine or any other disinfectant will not work well when water is turbid. The chlorine cannot always go through the suspended particles and may not get rid of organisms that cause sickness.

Table of Chlorine Dosages
1 gallon 5 drops
10 gallons 1/2 teaspoon
50 gallons 2 teaspoons
100 gallons 1 tablespoon
500 gallons 5 tablespoons
1,000 gallons 3/4 cup

* Household laundry bleach (5.25% chlorine concentration)

Contact Us

Private Drinking Water Program

Phone: 802-489-7339

Email: AHS.VDHEnvHealth@Vermont.gov

Last Updated: March 16, 2023