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Step-by-step Guide to Disinfect Your Water Well

Step-by-step Guide to Disinfect Your Water Well
Written by
Simple Pump
Published on
February 3, 2023

A Comprehensive Guide To Shocking Your Water Well

The image above shows Cryptosporidium, one of many possible contaminants of well water.

This is a step-by-step procedure for disinfecting your water well and plumbing systems using chlorine bleach (sodium hypochlorite). The information comes from a Fact Sheet by MN Dept. of Health.

Make sure the well pump isn't contaminating your well before adding it back after your disinfection process.

The Simple Pump is made with stainless steel and is Safe Water Drinking Act compliant.


Be sure to read this post fully before starting. You can also get a licensed well contractor or pump installer to disinfect your water well and system. This is recommended if you are not comfortable with this procedure, for complex water systems, severe contamination problems, or if have a Simple Pump alone, and no submersible.

For DIY, you may have a port you can add the bleach through. If so, that will make the job much easier.

Or if you have no port, you may have a regular well cap, a well seal, or a pitless well cap. If you have a pitless, it may be a type that is easily worked on, or one that a homeowner should not touch. If you DON’T have a port AND are uncertain about opening your well, you should seek local professional advice. We recommend you open your well yourself ONLY IF you already know how to and are comfortable doing that.



EXTREME CAUTION is advised when disinfecting a well, as you often will be working with electricity and water. Electricity can kill you. If you are not acquainted with working with electricity, seek professional advice.

Turn off electrical power to the pump by turning off the circuit breaker or unscrewing the fuse. If the breaker or fuse box has a “lockout” hasp to prevent someone from accidentally turning on the water pump circuit breaker, use it. Power should not be turned back on until STEP 6 or after the chlorine solution has been placed in the well.

Your safety precautions should include:

  • Turn off the pump circuit breaker before removing the well cap and while working on the well.
  • While the breaker is off, examine for chafed wire insulation or missing wire nuts and repair as necessary.
  • Wear rubber soled shoes or boots, preferably waterproof


Severe eye damage may result from contact with bleach or chlorine solution. Always follow the manufacturer’s use and safety directions.

  • Avoid eye and skin contact.
  • Wear protective goggles or a face shield and rubber gloves when working with the bleach or chlorine solution.
  • Handle and dispose of chlorine with care.
  • Do not mix chlorine with other chemicals, as mixing chemicals may form harmful gases.

Do not leave bleach bottles lying around – ingestion of bleach is the most common cause of poisoning of children in the U.S.


Underground well pits pose an extreme hazard, as they frequently contain a build-up of toxic gases or simply lack enough oxygen to sustain life. Access is limited, making quick escape difficult.

  • If your well is located in an underground well pit, DO NOT ENTER IT. Death can occur even in a shallow well pit.
  • Leave disinfection of wells in pits to professional, licensed well contractors, or pump installers.
  • Harmful gases may be generated during disinfection.
  • Avoid inhalation of fumes and make certain that enclosed spaces such as well rooms have adequate ventilation before starting disinfection.


The following procedure is for a well that has a submersible pump with either a removable well cap or a well seal with a threaded plug in it.

See STEP 4 to determine whether you have a well cap or a well seal. If the well has a sanitary seal, this procedure can only be attempted if a removable threaded plug in the sanitary seal allows access into the well.

If your well has a type of pump other than a submersible pump, is located in a well pit, is a flowing well, or has a sanitary seal without a threaded plug, you should have your well disinfected by a licensed well contractor or licensed pump installer.


► Bypass all other water system components, such as the dishwasher, washing machine, water softeners, water filters, and other water treatment or water-using devices. These may be damaged by chlorine. Since they may harbor organisms, it will be necessary to separately disinfect these other devices.

► Turn off and drain the water heater. Use caution to avoid scalds or burns. Follow procedures as described by the manufacturer or plumber.


The table below indicates the amount of laundry bleach (6.0 percent sodium hypochlorite or 5.7 percent available chlorine) that should be used for well disinfection.

Depth ofWell inFeetDiameter of Well0-5050-100100-2001-2 in.1/8 C.1/4 C1/2 C3-4 in.1/2 C1 C2 C5-6 in1 C2 C 1 Quart

► For wells greater than 100 feet deep or with well casing diameters greater than 6 inches, mix the bleach with 2 gallons of water.

► For wells greater than 200 feet deep or with well casing diameters greater than 6 inches, increase the amount of bleach proportionately. After this solution is poured into the well, it will provide a chlorine concentration of at least 50 parts per million.

► Sodium hypochlorite is the disinfectant found in laundry bleach and is the recommended product for well disinfection. Since bleach loses its disinfecting capacity over time it is important that a fresh container be used. Do not use laundry bleach that contains any fragrance or other additive.This table indicates the amount of laundry bleach (6.0 percent sodium hypochlorite or 5.7 percent available chlorine) that should be used for well disinfection.


► Place a large clean bucket near the well. Add 1 gallon of water and the amount of bleach indicated in the table and mix thoroughly.

► For wells greater than 100 feet deep or with well casing diameters greater than 6 inches, mix the bleach with 2 gallons of water.

► For wells greater than 200 feet deep or with well casing diameters greater than 6 inches, increase the amount of bleach proportionately.

► After this solution is poured into the well, it will provide a chlorine concentration of at least 50 parts per million.


► In situations where an initial disinfection has not worked, where there is considerable iron or other solids in the well, or where there is a significant nuisance bacteria problem, a more concentrated chlorine solution may be used.

► Multiply the quantities of chlorine listed in the table above by four and mix with 4 gallons of water (for example, a 4-inch diameter well that is 51-100 feet deep would need 4 cups of bleach mixed with 4 gallons of water).

► This will provide a chlorine concentration of at least 200 parts per million in the well and water system.

► Too strong a chlorine solution will reduce the effectiveness of disinfection. If the chlorine concentration greatly exceeds 200 parts per million, it can actually make the water too alkaline and reduce the effectiveness of the disinfection process.


► If your well has not been disinfected for many years, it may have considerable scale built up. Disinfecting with a strong chlorine solution can dislodge this scale and plug or damage your pump, and/or cause problems elsewhere in the plumbing system.

►You may wish to begin with a weaker solution of chlorine. If the water runs red or brown, pump it out on the ground surface without recirculating it back into the well as described in STEP 5.

► Once the color gets lighter, mix a new chlorine solution batch as described in STEP 2 and begin the process again.


► Before you proceed, double check that the power is turned off at the breaker box.

► If your well has a cap or seal with a plugged port, you can remove the plug and put it on a clean surface. Pour the chlorine solution through the hole. Using a funnel with a hose is best. Do not get bleach on the well cap or any wiring.
If there is no plug in the cap/seal, you should have the well disinfected by a licensed well contractor or licensed pump installer… unless, as stated above, you know EXACTLY how to open the well and are comfortable doing so.


► Pour the mixture into the well and avoid spilling on any wire connections. A funnel should be used for pouring the chlorine solution into small openings.

  • Be careful not to splash/spill the concentrated solution.
  • Wear gloves and goggles.
  • Do not use a siphon.


► Recirculating the chlorinated water mixes the water column thoroughly and distributes the chlorine. It helps to wash down the inside sidewalls of the well casing, pump wires, and drop pipe.

► Turn on the power to the pump.

► Connect a clean garden hose to a nearby yard hydrant or an outside faucet.

► Run the water out of the hose in an area away from the well for approximately 10 minutes until the water runs clear.

► You may notice that the water coming from the garden hose turns red, yellow, or brown. This is due to the chlorinated water precipitating iron from the water.

► The chlorinated water may also dislodge scale or rust from the sides of the well casing. Scale, iron, manganese, or other precipitated minerals may form when the chlorine is added to the system. These solids can cause clogging of faucet aerators, valves, water solenoids, and equipment using filters.

► Run the water out on the ground until the water runs clear. Additional chlorine solution may need to be added to the well.

► When the water coming from the garden hose is relatively clear, turn the water off, place the garden hose into the top of the well casing and run water into the well.

► After the chlorine smell is first detected from the garden hose, recirculate the water back into the well for about two hours.

► You can use chlorine test papers, such as those commonly used to check the chlorine in swimming pools, to provide a visual indication that chlorine is present.

► Turn off the power to the pump.

► Remove the garden hose from the well casing and replace the well cap or threaded plug in the well seal.

► Do not run discolored water through the household plumbing, and do not run it into a septic system.

► Since a strong chlorine solution may harm vegetation, dispose of the chlorinated water away from sensitive plants.

► Do not discharge water into a lake or stream as this may harm aquatic life.


► Turn on the power to the pump.

► Run chlorinated water through the entire plumbing system by running water to each fixture* one at a time until you smell bleach (or use chlorine test papers available at pool supply businesses) and then close the fixture.

► Do this for each fixture, including:

  • Cold and hot water faucets.
  • Toilets and shower/bath fixtures.
  • Any outside faucets or yard hydrants.

► Faucet aerators may need to be removed if clogging occurs from precipitated iron or loosened scale.

► Leave the chlorinated water in the system a minimum of two hours and preferably at least six hours or overnight.


►Run a garden hose from an outside faucet or yard hydrant to flush the chlorine out of the system. It can take 30 minutes to 24 hours or more to flush all of the chlorine from the well.

►Once the chlorine is gone from the well, open up each fixture one at a time until the chlorine smell is no longer present. This will purge the remaining chlorine from the water system. It should take just a few minutes to flush out the chlorine from the cold water lines. The hot water faucets will have to be run longer.

► In some cases, it may be quicker to drain the water heater(s) again. The small amount of chlorinated water flushed from the water pipes can be run into a septic tank.


► Chlorine can cause eye damage and skin irritation. In addition to not using the water for consumptive purposes, all potential water users need to be warned that a potentially dangerous concentration of chlorine is in the water system.

► Do not shower/bathe with water containing high levels of chlorine. You may wish to place a pail or bag over each faucet as a reminder.

► Do not run the chlorinated water into your septic system as this can kill many of the beneficial bacteria in the system. Also, the amount of water required to flush the well may hydraulically overload and damage the septic system.

► Since a strong chlorine solution may harm vegetation, dispose of the chlorinated water away from sensitive plants. Do not discharge water into a lake or stream as this may harm aquatic life.


► Return bypass valves to “on” or “service” position after following the manufacturer’s directions to disinfect these devices.

► Refill the water heater if applicable.

► Start the water heater.


► Make sure the chlorine has been removed from the water system. It is recommended that a sample be collected a couple days after the well is disinfected.

► Do not use the water for drinking, cooking, or food preparation until it tests free of coliform bacteria.


► It is a good idea to double check that the water is safe. After receiving the results of a satisfactory sample analysis, take another water sample approximately 30 days after the first sample and have the water retested.

► If coliform bacteria are detected again, re-disinfect the well using the same procedure. If the well and water system have not been disinfected for many years, they may need to be disinfected more than once.

► If multiple disinfections are unsuccessful, and coliform bacteria persist, contact a licensed well contractor or pump installer who can utilize special techniques and equipment to disinfect the well. The well may have to be physically cleaned or treated with other chemicals.

► The homeowner, well contractor, or pump installer should also inspect the well for any damage. Well casings can be cracked or well caps loosened if struck by vehicles or by garden or farming equipment.

► It is essential that any plumbing or well defects that could allow surface water or other contaminants to enter the well be corrected.

► If the well cannot be successfully disinfected, the source of the contamination should be determined if possible. If the source cannot be corrected or removed, the well may need to be sealed and a new well drilled.


► Water softeners, water treatment equipment, and water-using devices, such as dishwashers and washing machines should be disinfected according to the information provided by the manufacturer or contractor who installed it. If this information is not available, see the blog post on disinfecting water system components.

► If the disinfection information is unavailable, the following steps can be used, as recommended by the Water Quality Association, a not-for-profit international trade organization representing the household, commercial, industrial, and small community water treatment industry.


► Keep the unit on “bypass” until chlorine is flushed out of the system. To thoroughly disinfect the softener after all the chlorine is flushed from the system, add one-half cup bleach to the softener’s brine tank and run the unit through a regeneration cycle immediately. For a water softener that contains carbon, follow the directions below.


► For carbon filters and other cartridge water filters, remove and discard the old filter cartridge. Wash the sump and head with laundry detergent and bleach and rinse. Insert a new cartridge filter.

► For whole-house carbon tank filters or a water softener that contains carbon, empty the entire media bed. Thoroughly clean the empty unit inside and out with a laundry bleach and water solution. Re-bed the unit using new carbon or other media/carbon mix.


► Turn off the water supply to the RO unit and open the RO faucet to relieve pressure and drain the RO storage tank.

► Remove and discard the pre- and post-filters and remove the RO membrane element. Clean and disinfect the filter sumps, the filter heads, and the RO membrane housing and end caps.

► Fill the first pre-filter sump with water to within about 2 inches from the top and add 1 ounce (2 tablespoons) of unscented laundry bleach. Carefully reassemble this first pre-filter with the chlorine/water mixture but without its filter cartridge element in place.

► Reassemble all the remaining housings without their membrane element and filter cartridge elements in place.

► Open the water supply to the RO. Open the RO faucet and allow water to run until you can begin to smell the chlorine bleach. (If no chlorine bleach smell can be obtained, go back to bullet point three and increase the amount of laundry bleach added until a residual can be maintained throughout the system.)

► Close the RO faucet and allow the storage tank to fill and then remain full for 25-30 minutes.

► Open the RO faucet again and leave it open until the entire chlorine bleach smell is gone. Let the accumulated water in the RO storage tank drain completely.

► Turn off the water supply to the RO. Close the RO faucet after all the pressure has been relieved and the water flow stops.

► Install all new pre- and post-filter elements, using careful aseptic techniques so as to not recontaminate the RO system.

► Reinstall the RO membrane element in its housing. Fill the membrane element housing with water and 1 milliliter (20 drops) of laundry bleach. Reassemble this membrane element, chlorinated water, and housing unit.


High levels of chlorine over an extended period of time can degrade polyamide thin film composite (TFC) RO membranes, although significant degradations should not occur in these specified few minutes of chlorine contact time.

► Immediately reopen the water supply to the RO system and reopen the RO faucet. Let water drip from the RO faucet until the chlorine bleach smell has dissipated.

► Finally, close the RO faucet, let the storage tank completely refill, and discard the first full tank of water following the completion of this procedure.

A simplified video presentation of a well disinfection by Scott Hunt of Practical Preppers is available 

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