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Wells - Disinfecting after a Flood

Environmental Health

Chlorination disinfects your well by destroying bacteria and microorganisms and helps to remove iron, manganese and hydrogen sulfide (rotten egg smell).  You should always disinfect your well when a new well is drilled, the well has been repaired or a new pump installed or the well has been flooded or exposed to a bacterial contamination.   After disinfecting your well you should take a bacteriological sample from the well for 2 consecutive days.  Make sure to flush the well until there is no chlorine present before sampling.

If you are unsure if your well after a contamination or flooding, bring your water to a rolling boil for one minute and cool before use. Common unscented household bleach (4 to 6 percent active ingredient) can be used effectively as a chlorine disinfectant. Disinfect the water by adding 8 drops (about 1/8 teaspoon) of unscented household bleach per gallon of water, and then let it stand for 30 minutes.

FDOH recommends the following steps to disinfect a contaminated well:

  • If the water is discolored before adding the bleach, run the water until it is clear for up to 10 minutes.
  • Turn off and then drain your hot water heater; bleach is not effective in water above 105 degrees.
  • Remove and replace charcoal filters after the disinfecting process is completed.
  • To avoid adding contamination to the well during disinfection, clean the work area around the top of the well. Then remove grease and mineral deposits from accessible parts of the well head and flush the outside surfaces with 1/2 cup of unscented household bleach in 5 gallons of water.
  • Turn off the pump. Remove the cap or well plug on the rubber seal. There are many types of well caps and plugs. If you have questions, you should contact a licensed well driller. If you have a submersible pump, you may also want to contact a licensed well driller for advice on disinfection processes.
  • Check the bleach chart below and pour the recommended amount of unscented bleach (4 to 6 percent active ingredient) solution into the well. Try to coat the sides of the casing as you pour. If you get bleach on the pump or wiring, flush it thoroughly with fresh water to prevent later corrosion.


Well Depth in Feet                                                     Well Diameter in Inches

                                                                                     2”            4”                5”            6”

20’                                                                               1 cup       1 cup           1 cup       1 cup

30’                                                                               1 cup       1 cup           1 cup       2 cups

40’                                                                               1 cup       1 cup           2 cups     2 cups

50’                                                                               1 cup       2 cups         2 cups     3 cups

80’                                                                               1 cup       2 cups         1 qt         1 qt

100’                                                                             1 cup       3 cups         1 qt         1.5 qts

150’                                                                             2 cups     1 qt 2 qts        2.5 qts

200’                                                                             3 cups     1.5 qts         2.5 qts     3 qts


Conversions 8 oz = 1 cup /16 oz = 1 pint = 2 cups

24 oz = 3 cups / 32 oz = 1 quart / 48 oz = 1.5 quarts

64 oz = 2 quarts / 80 oz = 2.5 quarts / 96 oz = 3 quarts

  • Re-cap or plug the well opening and wait 30 minutes.
  • Turn on and, if needed, re-prime the pump. Open all of the faucets on the system one at a time. Allow the water to run until there is a noticeable smell of bleach. You may also want to flush the toilets. If you have outside faucets, you may want to direct the water away from sensitive plants. If you cannot detect a bleach odor, repeat the well disinfecting process.
  • Turn off all of the faucets and allow the bleach to remain in the plumbing system for at least 8 hours.
  • Backwash water softeners, sand filters, and iron removal filters with bleach water.
  • Again, open all the faucets and run the water until there is no bleach smell—for up to 15 minutes.

After disinfecting your well, the water needs to be tested to verify that it is safe to drink. Although unscented household bleach is effective against microorganisms, it will not remove chemical contamination that may have gotten into your well.