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Disinfection of Wells and House Plumbing Systems


The purpose of "shocking" or disinfecting a well and the piping system is to destroy any possible bacterial contamination present in the system. The disinfection process will kill only the bacterial contamination present in the system at the time of disinfection and will not kill bacteria that might be introduced at a later time. In other words, any time a well system is opened for repairs or additional plumbing (like softeners, filters or replacing a pump or pipes, etc.), the entire system should be re-shocked. Therefore, it is vital that the well be constructed so no new contaminants (soil, animals, insects or surface water) can enter the well after disinfection.

In order to achieve proper disinfection of the water system, the bacteria must be brought into contact and remain in contact with a chlorine solution of a sufficient strength for a minimum amount of time. These directions explain the proper way of doing this in order to kill coliform bacteria, which is an indicator of the microbiological quality of the water supply. If a well is disinfected and a second test shows the presence of coliform bacteria, this indicates inadequate disinfection or a problem somewhere in the water system or possibly a contaminated aquifer. The disinfection process can be repeated or an engineer or other qualified water system professional can be consulted for troubleshooting and/or disinfection. Multiple positive samples may indicate contaminated ground water and the need to install an ultraviolet light disinfection system to treat the entire house water supply.

Testing of the well water a few times each year is strongly recommended to ensure water quality meets drinking water standards for microbiological contaminants. Most water can be made microbiologically safe by bringing the water to a rolling boil for two minutes or by adding eight drops of household bleach to a gallon of water and letting it stand for 30 minutes.

One should always use caution when working with chlorine products. ALWAYS follow the manufacturer's safety directions. It is recommended that rubber gloves, protective clothing and safety goggles be worn. Wash immediately if you come into contact with chlorine. Electrical hazards also exist; it is recommended that the power to the well be turned off prior to any work being performed.

Determining the amount of bleach needed to shock the well:
In general, for clear well water use 3 cups of regular (unscented) bleach per 100 feet of depth of the well. For example, if your well is 300 feet deep, use 9 cups of bleach; if your well is 110 feet deep, use 3 cups, etc. Well water containing hydrogen sulfide (rotten egg odor), iron (brown water) or manganese (black water) will require additional bleach since chlorine is used up by these contaminants through a chemical reaction.

Adding the bleach into the well

Remove and inspect the well seal on top of the well casing (it should not be cracked and should fit snugly on the well casing). Some older wells may be buried which would require that the soil be removed to expose the top of the well casing so the seal can be accessed (buried wells are more susceptible to contamination; it is recommended that the well casing be extended to 12" above the ground surface). Dilute the bleach by about 50% and pour the bleach into well casing by having it wash down the inside of the casing. Attach a garden hose to an outside spigot and put the end of the hose into the well casing. Turn on the spigot and let the water in the hose run for about 1/2 hour into the well. After the 1/2 hour, smell the water coming out of the hose; if it does not smell of chlorine, continue to let it run into the well and smell it every so often until the chlorine odor is present. If a chlorine odor is not detected add more bleach until a chlorine odor is detected; this may be necessary due to hydrogen sulfide, iron or manganese in the well water.

Once the odor of chlorine is detected, turn off the hose. If you have a water softener, activated carbon or other water treatment system put it on bypass NOW so the chlorine will not damage the unit or be removed by it. (See the section at the end of these instructions titled "About Water Treatment Systems"). Turn on each water faucet in the house until you can smell chlorine; this is necessary in order to disinfect the whole house plumbing system, which may have been contaminated. Reinstall the well seal on the casing and let the system sit at least 8 hours or overnight. DO NOT use the water during this time, in order to get the best contact time in the pipes and well, and because the water will be highly chlorinated.

Flushing out the bleach after disinfection:

After disinfection it is necessary to flush out the highly chlorinated water so the water can be used for domestic purposes. It is important NOT to run the highly chlorinated water into the sewer system to avoid disrupting or overloading the system. It is recommended that the garden hose be used and the chlorinated water be flushed onto the driveway away from vegetation of value. Flush the well until no or only a slight chlorine odor can be detected. A swimming pool chlorine test kit can be used. Then go into the house and turn on all the faucets for 5-10 minutes to flush the highly chlorinated water out of the house plumbing system.

If you noticed a brown (iron) or black (manganese) discoloration of your water during disinfection, it is recommend that an empty load of laundry be run to ensure that all discolored water is flushed from the pipes supplying the washing machine. This problem is caused by chlorine reacting with iron and/or manganese in your water. This reaction creates a colored precipitate that can stain your clothing and plumbing fixtures.

Testing your water after disinfection:

Once you have disinfected the well, it will be necessary to test your water (again) to be sure the problem of bacterial contamination has been resolved. It is very important to WAIT 7-10 DAYS AFTER DISINFECTING YOUR WELL TO RETEST YOUR WATER. This amount of time is necessary in order to obtain a representative water sample from the aquifer. If a sample is collected before this amount of time and there is a problem with bacterial contamination, it may not show up, and you may risk the possibility of becoming ill from drinking your water.

The Dutchess County Department of Behavioral & Community Health has a list of several local laboratories that accept water samples from the public for a fee.  Please contact the individual laboratory for pricing, sample containers, sample collection directions, and hours of operation. If you need further assistance, call the Dutchess County Department of Behavioral & Community Health at 845-486-3404.


General instructions on how to collect a bacterial sample for testing are noted below

The cold water tap in the kitchen is the ideal spot for sampling drinking water. Avoid sites such as hydrants, drinking fountains, leaky taps, outside taps, basement taps, hoses, storage tanks, or dead end pipes. Fresh well water can be obtained by removing the strainer/screen, or filter from the faucet and letting the water run at least 5 minutes before collecting the sample. Do not open the bottle until the sample is to be collected. Remove the cap making sure not to touch the neck of the bottle or the insides of the cap or bottle. Hold the bottle at the base and fill to almost full without having the water overflow the bottle. Do not rinse the bottle out first! Replace cap immediately. Coliform sampling bottles may have a white powder or pellet in the bottle; this material is placed in the bottle to remove the chlorine residual after the bottle has been filled. It must not be rinsed out.

About Water Treatment Systems

Water Softeners 
For proper disinfection of water softening systems, we recommend that you not only disinfect them separately from the well, but also you disinfect them regularly, according to the manufacturer's instruction manual (which should come with the unit). This way you do not run the risk of damaging the softening unit.

Activated Carbon Units 
Whole house activated carbon units MUST be bypassed since this type of treatment system will remove chlorine. Activated carbon filters can not be disinfected therefore should be followed with a disinfection system such as an ultraviolet light disinfection unit on a permanent basis.

Other Treatment Systems 
Other treatment systems, such as greensand filters and sand filters, should be bypassed and disinfected separately from the well according to the manufacturer's instruction manual. Regular disinfection of these types or treatment systems is also recommended.

Disinfection Systems 
A disinfection system may need to be installed if Total Coliform testing indicates that the ground water is contaminated. Two common disinfection systems are the ultraviolet light and chlorination systems. The ultraviolet light system is simpler to operate, however, may require pretreatment to ensure the water is clear enough for this system to work properly with little maintenance. Maintenance usually consists of replacing the bulb and cleaning the unit annually. More frequent cleanings may be required. A chlorination system consists of a small pump used to inject a small quantity of bleach into the water and a detention tank (that provides 15 minutes of detention time) to ensure a complete kill of pathogenic organisms. Maintenance on these systems is usually higher and the water will contain a low chlorine residual. The type of system chosen should take into consideration any other water quality concerns and their treatment requirements.

For more information on safe drinking water:
Safe Drinking Water
Safe Drinking Water (.pdf)