September 1, 2005 Page 1 of 6

Disinfecting Wells Following an Emergency 

If you suspect that your well may be contaminated, contact your local or state health department for 

specific advice. If you do not get your water from a well, see Keep Food and Water Safe for information on 

disinfecting your water. 

IMPORTANT: Fuel and other chemical releases and spills are common during flood events. If your water 

smells like fuel or has a chemical odor, contact your local or state health department to request a 

chemical analysis of your water before using it. Until you know the water is safe, use bottled water or 

some other safe supply of water. 

 

Safety Precautions

You will need to clear hazards away from wells before cleaning and disinfecting wells after floods and 

other natural disasters. The following precautions will help you do that safely: 

1. Before beginning any action, carefully inspect the area around the well for electrical and physical 

hazards. Those may include broken power lines on the ground or in the water; sharp metal, glass, 

or wood debris; open holes; and slippery conditions. 

2. Wear thick rubber-soled shoes or boots to protect against electrical shock. 

3. Turn off all power to the well area before clearing debris. Inspect all electrical connections for 

breaks in insulation and for moisture. Turn power back on only if all connections appear unbroken

and dry with no opportunity for shock. 

4. Do not turn on any electrical equipment if there is a persistent smell of fuel such as gasoline

coming from the well head. Allow the well to vent. If the smell persists, contact your local or state 

health department. Do not continue with disinfection of the well until the contamination in the well 

has been removed 

5. Before beginning work on the well, clear debris away from it to avoid inadvertently moving debris

into the well. 

6. When clearing debris from large-diameter wells (36 inches [approximately 90 centimeters (cm)] or 

greater), use grappling hooks, nets, and long-handled scoops to remove debris. Do not enter the 

well pit. Gases and vapors can build up in well pits, creating a hazardous environment. 

Follow these additional precautions as you prepare to disinfect the wells: 

• Chlorine solutions can cause chemical burns. Use rubber gloves, protective eye wear, and 

waterproof aprons or rain gear when working with chlorine solutions.

• When mixing and handling chlorine solutions, work in well ventilated areas and avoid breathing 

vapors. When working in closed spaces, use electrical fans to provide fresh air. 

• Warn users not to drink or bathe in water until all the well disinfection steps have been completed 

and the well has been thoroughly flushed. 
Disinfecting Wells Following an Emergency 

 (continued from previous page) 

Here are some general instructions for disinfecting wells that may have become contaminated by harmful 

microorganisms in floods or other natural disasters. 

Steps to Disinfect Drilled, Bored, or Dug Wells 

Chlorination is a process of flushing your well water system with a chlorine solution to kill bacteria and 

other microorganisms. This process is recommended after floods and when a well has tested positive for 

bacteria. It is an effective method to eliminate germ contamination, but if problems exist with faulty well 

construction or groundwater contamination, chlorination is only a temporary solution. If contamination

persists, further investigation may be needed to determine the problem.

The disinfection process can take from a few hours to a few days to complete. Make sure you store 

enough water to meet your household needs before you start this process. 

Read the safety precaution section before starting the disinfection procedure. 

Disinfection Procedure 

Step 1. Scrub or hose off foreign material from the well curbing or casing. If the well cover was not 

properly sealed and flooding has occurred, sand and silt may have deposited in the well, requiring 

more cleaning. 

Drilled and bored wells: Remove the well cover and thoroughly clean the well to remove all 

debris. Special tools or pumps may be required to remove silt and sand. Heavy deposits of silt 

and sand may damage well pumps if not removed before the pump is started. If sand and silt are 

present, remove the pump and clean it thoroughly before using.

Dug wells: Remove the well cover and thoroughly clean the well to remove all floating debris. If 

the well is lined, scrub the sides of the well with a brush and a strong solution of chlorine and 

water. Empty polluted water and debris from the well using buckets or pumps. If sand and silt 

are present, remove the pump and clean it thoroughly before using. Rinse well walls by pouring 

water along the edges. Empty polluted rinse water from the well again, then allow it to refill.

Caution: In areas without electrical power, a portable generator may be needed to operate 

pumps and equipment. Read the safety instructions before turning on a generator, pumps, or any 

electrical equipment. 

September 1, 2005 Page 2 of 6
Disinfecting Wells Following an Emergency 

 (continued from previous page) 

Step 2. Pump or bail water out of the well until the water is clear. If you have a low-yield well, empty at

a slower rate. If available, use outside faucets to drain water from the well. Do not pump

contaminated water into any existing pressure tank. Instead, disconnect piping between the 

pressure tank and pump to allow contaminated water to flow away from the well and tank. 

Step 3. Using the table below, calculate the amount of bleach granules or unscented liquid to use. To 

determine the exact amount, find the corresponding well diameter in the left column. Then match

the amount of bleach needed for the amount of time the concentration will remain in the well.

Multiply the amount of bleach needed by every 10 feet of water in the well. 

For example, a well 8 inches in diameter requires 31⁄2 fluid ounces of unscented bleach (for a

retention time of 8 hours at 50 parts per million [ppm]) per 10 feet of water. If the water in the 

well is 30 feet deep, multiply 31⁄2 fluid ounces by 3 to determine the amount of bleach required 

(31⁄2 x 3 = 11.5 fluid ounces). In a clean bucket, add this total amount of bleach to about 5

gallons of water (or mix this in 5 gallons of water). 

If you are unsure about the depth of your well, check the well head and casing to see if a tag

indicates the well depth. If a tag is not available, contact neighbors to see if they know the 

depths of their wells. Well depths are usually similar in neighborhoods. If you are still unable to 

determine the depth of your well, make your best educated guess, then increase the suggested 

amounts of chlorine by 50%. 

Système International d’Unités (metric): A well 20.0 cm (8 inches) in diameter requires roughly

103.5 milliliters (mL) of unscented bleach per 3 meters of water. If the water in the well is 

approximately 9.1 meters deep, multiply 103.5 mL by 3 to determine the amount of bleach 

required (103.5 X 3 = 310.5 mL). In a clean bucket, add this total amount of bleach to about 19 

liters of water.

Step 4. Pour the chlorine solution in the well in a circular pattern to ensure contact with all sides of the 

casing or lining of the well. If bored and dugs wells have no casing or lining, pour the solution 

down the center of the well hole. If possible, recirculate the water by connecting a garden hose to 

an outside faucet and place the other end in the well. Allow water to run for approximately 15

minutes to ensure the chlorine solution is mixed in the well. 

Step 5. For wells connected to a plumbing system, open all inside and outside faucets and pump water 

until you notice a strong odor of chlorine at each faucet. If you do not smell chlorine after 

running all faucets for 15 minutes, increase the amount of chlorine by one-half of the original

amount used and repeat the procedures. 

Stop the pump and allow the chlorine solution to remain in the well and plumbing system. Refer 

to the table in the “Sampling After Disinfection” section to match amounts of chlorine solution 

and disinfection times. It is preferable for the solution to remain in the well for 8 hours or 

overnight, if possible. Do not leave chlorine in wells more than 24 hours because it may affect

some pump parts. 

Step 6. After the disinfectant has set in the well for the recommended period, turn on the pump, attach a 

hose to an outside faucet, and direct the water to a designated area away from the well. The 

water in the well contains high concentrations of chlorine that can be harmful to plants, septic 

tanks, and streams. Empty the water in an area where plants or streams will not be harmed. 

Continue running the water until the chlorine odor disappears, then drain the remainder of bleach 

September 1, 2005 Page 3 of 6
Disinfecting Wells Following an Emergency 

 (continued from previous page) 

in the plumbing system from the inside faucets. With low-yield wells, empty plumbing at a slower 

rate to avoid over pumping. Some wells may require that you stop for periods to allow the well to 

refill. Depending on the depth and size of the well, this process may take hours to a day or 

longer.

Water from wells with no plumbing system can simply be pumped or removed in buckets until the 

chlorine odor disappears. 

 

Sampling After Disinfection 

Until water has been tested, any water for human consumption should be boiled (roiling boil for 1 minute),

or an alternative water source used. Wait at least 2 days after disinfection to ensure that the chlorine has 

been thoroughly flushed from the system. Then sample the water for total coliform and either E. coli or 

fecal coliform bacteria to confirm that the water is safe to drink. Contact the local health department to

have your water sampled and tested or contact your state laboratory certification officer to find a certified 

lab near you. You can also get this number from the U.S. Environmental Protection Agency’s Safe Drinking 

Water Hotline (800-426-4791 or www.epa.gov/safewater/labs/index.html). 

If the sample results show no presence of both total coliform and E. coli or fecal coliforms, the water can 

be considered safe to drink from a microbial standpoint. Follow up with two additional samples, one in the 

next 2 to 4 weeks and another in 3 to 4 months. To check the safety of your water over the long term,

continue to monitor bacterial quality at least twice per year or more often if you suspect any changes in

your water quality. 

If sample results indicate the presence of total coliform and E. coli or fecal coliforms, repeat the well 

disinfection process and resample. If tests continue to show the presence of bacteria, contact your local 

health department for assistance. 

September 1, 2005 Page 4 of 6
Disinfecting Wells Following an Emergency 

 (continued from previous page) 

September 1, 2005 

Amount of Chlorine Needed Per 10 Feet (3.1 Meters) of Water in Well* 

Amount of 5.25% Sodium 

hypochlorite 

(Unscented Laundry Bleach) 

Standard/SI

Amount of 65% Calcium Hypochlorite 

(Chlorine Granules) 

Standard/SI

Disinfection time for concentration of disinfectant 

Inside 

Diameter of

Well Casing 

(Standard/SI

)

100 ppm 

for 

2 hours 

50 ppm for 

8 hours 

25 ppm for 

24 hours 

100 ppm 

for 2 hours 

50 ppm for 

8 hours 

25 ppm for 

24 hours 

11⁄4 inches 

or 3.18 cm 

1⁄8 fluid 

ounces 

or 3.7 mL 

3⁄4 teaspoon 

or 3.7 mL 

1/3 

teaspoon 

or 3 mL 

2 inches 

or 5.08 cm 

1⁄2 fluid 

ounces 

or 14.79 

mL 

1⁄4 fluid 

ounces 

or 7. 39 mL 

1⁄8 fluid 

ounces 

or 3.7 mL 

3 inches 

or 7.62 cm 

1 fluid 

ounces 

or 29.57 

mL 

1⁄2 fluid 

ounces 

or 14.79 mL 

1⁄4 fluid 

ounces 

or 7.39 mL 

4 inches 

or 10.16 cm 

11⁄2 fluid 

ounces 

or 44.36 

mL 

3⁄4 fluid 

ounces 

or 22.18 mL 

3⁄8 fluid 

ounces 

or 11.09 mL 

Not practical to use chlorine

granules for these smalldiameter well casings 

6 inches 

or 15.24 cm 

4 fluid 

ounces 

or 118.29 

mL 

2 fluid 

ounces 

or 59.15 mL 

1 fluid 

ounces 

or 29.57 mL 

1⁄4 ounce 

or 7.09 

grams 

1⁄8 ounce 

or 3.54 

grams 

1/16 ounce 

or 1.77 

grams 

8 inches 

or 20.32 cm 

7 fluid 

ounces 

or 118.29 

mL 

31⁄2 fluid 

ounces 

or 103.51 

mL 

13⁄4 fluid 

ounces 

or 51.75 mL 

1⁄2 ounce 

or 14.17 

grams 

1⁄4 ounce 

or 7.09 

grams 

1⁄8 ounce 

or 3.54 

grams 

10 inches 

or 25.40 cm 

10 fluid 

ounces 

or 295.74 

mL 

5 fluid 

ounces 

or 146.87 

mL 

2 fluid 

ounces 

or 59.15 mL 

3⁄4 ounce 

or 21.26 

grams 

3⁄8 ounce 

or 10.63 

grams 

3/16 ounce 

or 5.32 

grams 

12 inches 

or 30.48 cm 

2 cups 

or 473.18 

mL 

1 cup 

or 236.59 

mL 

1⁄2 cup 

or 118.29 

1 ounce 

or 28.35 

grams 

1⁄2 ounce 

or 14.17 

grams 

1⁄4 ounce 

or 7.09 

grams 

18 inches 

or 25.72 cm 

41⁄2 cups 

or 1.06 L 

21⁄4 cups 

or 532.32 

mL 

11⁄8 cups 

or 266.16 

mL 

21⁄2 ounces 

or 70.87 

grams 

11⁄4 ounces 

or 35.44 

grams 

3⁄4 ounces 

or 21.26 

grams 

2 feet 

or 60.96 cm 

71⁄2 cups 

or 1.77 L 

33⁄4 cups 

or 887.21 

mL 

17⁄8 cups 

or 443.60 

mL 

41⁄2 ounces 

or 127.57 

grams 

21⁄4 ounces 

or 63.79 

grams 

11⁄8 ounces 

or 31.89 

grams 

3 feet 

or 91.44 cm 

171⁄2 cups 

or 4.14 L 

83⁄4 cups 

or 7.01 L 

43⁄8 cups 

or 1.04 L 

10 ounces 

or 283.5 

grams 

5 ounces 

or 141.75 

grams 

21⁄2 ounces 

or 70.87 

grams 

*Notes: 1 heaping tablespoon of 65% chlorine powder=1⁄2 ounces; 8 fluid ounces=1 cup. 

cm=centimeter; L=liter; mL=milliliter; ppm=parts per million; SI=Système International d’Unités 

(metric). 

Page 5 of 6
Disinfecting Wells Following an Emergency 

 (continued from previous page) 

September 1, 2005 Page 6 of 6

• World Health Organization (WHO) South-East Asia Earthquake and Tsunami List of Guidelines for 

Disinfection Issues and Concerns 

Bored and dug wells can be difficult to disinfect because of how they are constructed. Many are shallow 

and have no lining or casing, which can allow contaminants to enter the well hole from upper soil levels. If

contamination problems continue, consider upgrading the existing well or drilling a new well.

Water softeners may be damaged by the disinfection process because of the large amounts of chlorine 

used. Follow your manufacturers’ instructions for appropriate methods to disinfect your softener unit. You 

may need to bypass the unit until the disinfection process is complete. 

Related Resources 

Health Emergencies: Water

(http://w3.whosea.org/EN/Section23/Section1108/Section1835_8188.htm) 

• WHO South-East Asia Earthquake and Tsunami Web Site: Household Water Treatment and Safe 

(http://www.who.int/household_water/resources/emergencies.pdf) 

Storage Following Emergencies and Disasters

• WHO: The International Network to Promote Household Water Treatment and Safe Storage

(http://www.who.int/household_water/en/) 

• U.S. Environmental Protection Agency Advice on Flooded Wells

(http://www.epa.gov/safewater/privatewells/whatdo.html)

For more information, visit www.bt.cdc.gov/disasters, 

or call CDC at 800-CDC-INFO (English and Spanish) or 888-232-6348 (TTY).