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 Well

Follow the steps below to disinfect your well if bacteria were detected in your water, your well was repaired (including replacing the pump), you installed a new well, or there is a hydrogen sulfide (rotten egg) smell in your water system.

Before you disinfect your well

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

2. Consider testing for nitrate and chloride.

  • If nitrate or chloride are in your water, this might mean that a septic system or nearby farm could be the source of contamination.

3. Gather the materials you will need.

  • Rubber gloves and eye protection
  • Household liquid chlorine bleach that contains no scents or additives
  • 5-gallon bucket
  • Small brush
  • Garden hose
  • Measuring cup

4. Find out the depth and dimensions of your well.

  • For drilled wells, most have an “ID” tag attached to the casing. This number can be used to search this database to find the depth of the well. If you do not know the depth of the well, and there is no well ID tag, contact the person or company who drilled your well or reach out to a local well driller.
  • For dug wells, you will need to know the volume of water stored in the well. If you don’t know the volume, you can calculate it. 
    • For a cylindrical well, find the radius (distance from the center to the outer circle) and the depth and use this calculation: volume in gallons = (radius)2 (in feet) x 3.1415 x depth (in feet) x 7.5

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

  • 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. Note: boiling water may concentrate other contaminants, like nitrate, in your well. Only boil your water if you know there are no other contaminants in your water. Learn more about testing for drinking water contaminants.

6. 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 and cause your water to become contaminated.
  • 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 guide to disinfecting your well

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 or use 1/2 cup of bleach for every 10 feet of depth for a standard 6-inch diameter drilled well or for dug wells use 1 cup of bleach for per 30 gallons of water storage. 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. Reseal the well and (if applicable) 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. Remove any screens on your faucets as they can become clogged by debris dislodged during the disinfection process.
  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 8 to 12 hours to give the chlorine time to disinfect your system.
  12. After at least 8 hours, 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. Flushing large volumes of chlorinated water into your septic system may damage it. 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 running both 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 2 to 3 days after the chlorine smell is gone. Order the bacteria test (Kit A) from the Health Department Lab.
  16. Continue to either boil your water or get water from a safe source until no bacteria are 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 a video to learn how to shock chlorinate your well

This 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.

How to Disinfect Your Spring

If you are uncomfortable or unable to follow these steps or need help with disinfection, contact a local well driller or water quality expert.

Shock chlorination of springs is difficult and often doesn’t work. This is because the water often runs through the spring box too quickly for the chlorine to kill the bacteria. If bacteria are still present after shocking, the Health Department recommends a continuous disinfection system, such as a UV light.

Caution: Do not disinfect the spring box if the spring overflow (the water that does not go to your house) reaches a stream, pond or wetland area. Chlorinated water may kill fish and harm the environment. If the spring box overflows from a flood event, wait for the water level to go down before shocking.

Follow the steps below to disinfect your spring if bacteria were detected in your water, your spring system was repaired, or if the system was flooded or contaminated.

Before you disinfect your spring

1. Visually inspect your spring system and make any repairs.

  • Look for and fix any sources of bacterial contamination in and around your spring, such as visible cracks, blockages at the inlet or outlet, debris inside the spring box, loose caps or fittings, etc.

2. Consider testing for nitrate and chloride.

  • If nitrate or chloride are in your water, this means a septic system or nearby farm could be the source of contamination.

3. Gather the materials you will need.

  • Rubber gloves and eye protection
  • Household liquid chlorine bleach that contains no scents or additives
  • Fast-dissolving 65-70% calcium hypochlorite pellets with no algaecides, chlorine stabilizers/conditioners, acids, or other disinfectants (available at pool supply or hardware stores)
  • 5-gallon bucket
  • Small brush
  • Garden hose
  • Measuring cup

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

  • 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. Note: boiling water may concentrate other contaminants, like nitrate, in your spring. Only boil your water if you know there are no other contaminants in your water. Learn more about testing for drinking water contaminants.

5. Flush your system if the water appears cloudy or full of sediment.

  • Turn on an outside spigot and flush water until it begins to run clear. Be careful not to pump the spring dry, which could damage it and cause your water to become contaminated.
Step-by-step guide to disinfecting your spring

Download or print the step-by-step guide to disinfecting your spring

You will be adding calcium hypochlorite pellets and chlorine directly to your spring. 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, calcium hypochlorite pellets (with no algaecides, chlorine stabilizers/conditioners, acids, or other disinfectants), 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. If pump-operated, turn off power to the pump.
  4. Calculate the amount of disinfectant you will need for your spring. Use fast-dissolving 65-70% calcium hypochlorite solid pellets (with no additives). Estimate the volume of water in the spring box. You will need 3 ounces of pellets for every 100 gallons of water. For many spring boxes, 2 feet in depth is 100 gallons of water, but you may need to modify this calculation based on your spring. One cubic foot of water is equal to 7.5 gallons.
  5. Flush and drain the spring box and remove debris and sediment. Scrub the interior of the spring box with a strong chlorine solution (1/2 cup of plain, unscented, liquid laundry bleach mixed in 5 gallons of water.
  6. Allow the spring box to fill with fresh water. Add 3 ounces (85 grams) of the calcium hypochlorite pellets for every 100 gallons of water in the spring. Keep the overflow outlet open.
  7. Go to the faucet inside your home that is farthest from the spring 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. Remove any screens on your faucets as they can become clogged by debris dislodged during the disinfection process.
  8. Leave the chlorinated water in the plumbing for 8 to 12 hours to give the chlorine time to disinfect your system. If the flow rate is too high to keep the chlorine solution for 8 to 12 hours, use a tank to feed the chlorine solution into the spring box continuously for at least eight hours.
  9. After 8 to 12 hours, 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. Flushing large volumes of chlorinated water into your septic system may damage it. You may want to run the water at less than full flow or turn the tap off periodically to allow the spring to recharge so it does not run dry.
  10. Flush the taps inside your home by running both the hot and cold faucets until you no longer smell bleach.
  11. Remove, clean, then replace any screens on your faucets as they can become clogged by debris dislodged during the disinfection process.
  12. Retest your water 2 to 3 days after the chlorine smell is gone. Order the bacteria test (Kit A) from the Health Department Lab. You may want to retest 2 to 4 weeks later to ensure that bacteria do not continue to enter the spring.
  13. Continue to either boil your water or get water from a safe source until no bacteria are detected.
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?

It may take multiple rounds of disinfection and flushing to resolve the problem. Consider permanent treatment for your water supply. Make sure any treatment device is certified by the National Sanitation Foundation (NSF). The Health Department recommends contacting a water treatment specialist to get the most up-to-date treatment information and estimates. It is usually a good idea to get estimates and treatment recommendations from more than one water treatment specialist before you make your decision. Once the system is installed, you will need to maintain it. Be sure to ask for maintenance cost estimates, too.

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 [email protected].

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
wATER vOLUME LIQUID BLEACH*
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: [email protected]

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