How to Disinfect Your Water Well with Chlorine

If there’s been a flood or unexpected groundwater contamination from a spill, you may need to disinfect your well water. While you should call a professional to do the disinfection, it’s good to know the basics of how it works.


Click here for step by step instructions for well chlorination.


When there’s a flood, your well can become contaminated by floodwater that’s been tainted by sewage from flooded septic systems, bacteria or fertilizer from nearby farms.


Flood water can also carry debris that can cause structural damage and loosen hardware or damage the cap. Following flooding, the New Hampshire Department of Environmental Services recommends checking the well structure to see if there are cracks or structural problems that would allow bacteria to enter the well. If those issues aren’t addressed and you disinfect, the contamination is likely to return. So, if your well is flooded, it’s a good idea to assume it has been contaminated and take the proper precautions.


Until you can have your water tested, it’s best not to use the water from the well, so look for alternative sources of fresh, clean water. If none are available, you can boil your well water for five minutes before use, according to the Massachusetts Office of Energy and Environmental Affairs.


Disinfecting your well water with chlorine


You’ll first need to flush your home’s water system and the well through your outdoor faucets to remove rust, dirt or sediment because they trap bacteria that chlorine can’t reach. Flush the well by pumping water until it’s no longer discolored. Flush the pumping system and the plumbing until the water from the faucets runs clear.


Next is disinfection with chlorine, the standard chemical used for disinfecting water systems (except for treatment systems). The concentration of chlorine used depends on the degree of contamination. The NH DES has published guidelines on how to calculate how much chlorine to use.


Your well water professional will open the cap and pour the chlorine into the well, mixing by adding water from an outdoor hose and recirculating for at least 15 minutes. The water will circulate through the pressure tank and plumbing system – you will be able to smell when it has reached all of the taps or you can use a test kit. Leave the treated water in the well and pipes overnight and be sure not to drink, cook, bathe or shower with it.


The next morning the well water will be flushed by turning on an outside spigot with a hose attached until there’s no more chlorine smell and/or the concentration is less than 1.0 mg/L.

Once the chlorine is all gone, the water can be tested. If the bacteria is gone, the water will be safe for drinking again. If not, disinfection may need to be repeated.  If the contamination keeps recurring, a permanent disinfection system, such as an ultraviolet system that disrupts the reproduction ability of bacteria, may be necessary.  It’s best to check with experts, like the staff at Skillings & Sons, for advice on how to disinfect and maintain your well.