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How to Clean Well Water Systems

By China Zmuida ; Updated July 27, 2017

Cleaning your well water system is necessary to purge your well system of harmful bacterias and minerals such as iron and sulfates. Cleaning your well system is a time-consuming procedure. Cleaning your system requires a process known as chlorination. Once you have completed the task, you'll need to test your water to verify that it is free of bacteria, as well as chlorine.

Put on a pair of rubber gloves and goggles. Dilute your bleach. For every 1 cup of bleach that is used, mix the bleach with 12 cups of water. You'll need at least 1 gallon of bleach to thoroughly flush out a well system.

Check to see if your well contains a sanitary seal or if your well is dug directly into the ground. Remove the air vent if your well contains a sanitary seal. If your well is dug into the ground, you can remove the cover that is placed over your well.

Take your bleach solution and gently pour the solution into your well system. Take care when pouring the solution so as to not splash any bleach onto your skin.

Take a hose from your outdoor faucet, and place the hose into your well casing. According to the Environmental Protection Agency, you should run the hose until you can smell chlorine emanating from the hose.

Turn on all indoor and outdoor faucets. Leave your faucets on until the odor of chlorine can be smelled. Once you smell chlorine, turn all faucets off.

Wait one full day prior to turning your faucets back on. Take an outdoor hose and pull it away from any outdoor vegetation or waterways (such as streams or lakes). Turn the hose on for at least two hours, or until the smell of chlorine disappears.

Turn all your faucets on in your home until chlorine smell vanishes. Test your home for bacteria and chlorine at least one week after completing the chlorination process.


According to the University of Minnesota, use a household bleach that contains at least 5.25 percent of hypochlorite. If your well system contains a water treatment system, turn the water treatment system over to bypass prior to chlorinating your well system. Use bottled water to drink and cook with during the chlorination process. Chlorinate your well water system at least once a year.


Don't use bleach that is scented. Don't drink, bathe or cook with your well water during the chlorination process.

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