Photograph of a water pressure tank control valve Water Treatment Equipment Disinfection Procedures
How to disinfect a water softener, water filter, water heater, water pressure tank, or similar equipment

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Water tanks, water treatment equipment & similar plumbing system disinfection procedures & warnings:

This article gives step by step procedurs to disinfect or shock or sanitize water supply system components such as the water tank, water softener tank, water heater, water filters, activated charcoal systems, water softeners and sulphur removal systems.

We repeat important well disinfection notes about adjusting the pH of well water & the pH of well disinfectant solution to assure adequate disinfection, & we repeat important safety warnings about handling chlorine or adding chlorine to water containing hydrogen sulfide H2S.

Page top sketch illustrating both deep and shallow water well construction and depths is provided courtesy of Carson Dunlop Associates.

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Special Chlorination, Shocking, Sanitizing Procedures for Water Filters, Water Heaters, Water Softeners, and Water Tanks

Water heater drain (C) Daniel FriedmanReader Question: 

I would like to know when I chlorinate my well should I bypass the water softener and any filter in the line.

Also why does it say to turn on just the cold water? - Jerry Highsmith


We recommend these added water filter, water softener, and hot water heater details that may be helpful when shocking or chlorinating a well or when addressing an odor or sanitation problem in building water equipment such as water tanks, water softener brine tanks, or water heaters that need to be sanitized due to bacterial or similar contamination.

Article Contents

Bypass Equipment During Well Disinfection or When Disinfecting Individual Water Equipment

Water filters & activated charcoal water treatment equipment bypass during well disinfection

Take out the water filter cartridge then close up the canister, but do not put it on bypass. Let the chlorinated water run through the canister to sterilize and clean it, then install a new filter after all chlorine-smelling water has been flushed from the system.

Watch out: if you fail to bypass activated charcoal type water treatment equipment you may have difficulty removing the chlorine or other disinfectant and its odors from the building water supply. And if the charcoal filter system has itself been exposed to contaminated water you will most likely need to replace the filter or media with new, fresh, sanitary material.

Water softener bypass during well shocking

Bypass the water softener for the same reason we explain below about water heaters, and with the same exception as below.

Water heater bypass during well disinfection

Bypass the water heater when chlorinating the well for this reason: if you put chlorine-treated water inside the water heater, because incoming water in the water heater tank keeps mixing with what's already in the tank, it is difficult to flush all of the chlorinated water back out of the water tank without running a very large volume of water through the system.

Watch out: Also heating water that contains a high level of chlorine might produce potentially dangerous chlorine gas coming out of a hot water faucet.

If your water heater piping does not make it easy to bypass the actual water heater while running chlorinated water through both cold and hot water piping, then you might want to just run cold water in the building.

When flushing chlorinated water out of a well, it's fine to run that water through both hot and cold water piping and fixtures if you can bypass your water heater tank itself. That helps sanitize all of the building piping. But if you cannot bypass your water heater, you can have trouble getting all of the chlorinated water out of the water heater tank unless you first run cold water until there is no chlorine or bleach odor, then stop and drain any chlorinated water from the water heater tank.

When to Disinfect Water Tanks, Softener Brine Tank, Pressure Tank, Water Heater Tank

Exception - When to Run Chlorinated Well Water (during well shocking) through a Water Softener or Water Heater or Water Pressure Tank

You might want to run chlorinated water through a water heater tank or water softener tank from the shocked well during well disinfection if you suspect that those devices have been contaminated, such as by bacteria during area flooding, or in the case of a water heater, by bacteria that can form inside of a hot water tank. In that case, however, it may be easiest to simply drain the heater or softener tank completely, manually, after it has been treated (chlorinated) rather than trying to flush it out by running through the many times its actual water volume that would otherwise be required.

Watch out: be sure your water heater has been turned OFF and has cooled down to at least room temperature before trying to run chlorine through it. Heating water that contains a high level of chlorine might produce potentially dangerous chlorine gas coming out of a hot water faucet. More information is

It won't hurt the water heater or water softener equipment itself for a dilute amount of chlorine in water to remain inside it, (after all this equipment is used in some homes where a chlorine injection system constantly places a small amount of chlorine into the building water supply).

Because chlorine is volatile, eventually it will be dissipated as water is used or left in an open container (for use) in the building. See DRINKING WATER - EMERGENCY PURIFICATION for details.

How to Disinfect a Water Heater, Water Softener, Water Pressure Tank or similar equipment, 12-step guide

Iron stains on bathroom sink (C) D Friedman

OPINION: these steps provide some suggestions if it is necessary to sanitize or disinfect building water equipment such as the tanks or containers formed by a water heater, water softener, or pressure tank.

  1. Supply sanitary drinking water for equipment flushing; otherwise even though you clean and sanitize your equipment you risk renewing its contamination. If you're unsure about the safe potability of your water supply have it tested.
  2. Shut off water supply to the to-be-cleaned equipment
  3. Turn off the equipment if it uses power, such as a water softener, water heater, water pressure tank (and well pump)
  4. Drain the tank, heater, softener brine tank, etc.. it to remove sediment, scale, other debris. The drain procedure will remove pressure and then empty the vessel. For some closed vessels such as water pressure tanks and water heaters, you may need a trick or two to let air into the vessel so that you can drain it. Try opening a nearby water outlet valve or you might open an air inlet valve (on a bladderless water pressure tank but not one that uses an internal bladder), or a pressure relief valve on a water heater.
  5. Clean the tank, water heater, pressure tank or similar equipment as much as you can.
    • If you are sanitizing a cartridge-type water filter we suggest removing and throwing the old filter cartridge away; install a new filter cartridge after the system has been disinfected.
    • To disinfect or sanitize a water softener, be sure to also
      See SANITIZE the BRINE TANK & WATER CONDITIONER that is found in this longer article: SOFTENER CLEANING & SANITIZING that also discusses iron removal. Iron in water tanks, heaters, softeners can be a source of odors as well as staining.
    • Watch out: for a water softener you may need to replace the resin or use a resin-cleaning compound.
  6. Re-fill the tank or equipment with fresh clean water then turn off its water supply again.
  7. Add sufficient disinfectant to reach an adequate concentration.
    • How much bleach? Based on the concentrations given in our well chlorination & disinfection article cited below, that table gives cups Clorox or 2 oz. of granules in a 100 foot well (that is 100 ft. of water in a 6-inch casing). As there are about 1.5 gallons in a foot of 6-inch well casing, that computes to
      3 cups of Clorox household bleach in 100 x 1.5 gallons per foot or 3 cups of household bleach to 150 gallons of water
      or about 1 cup of Clorox household bleach in 50 gallons of water.
    • See WELL CHLORINATION & DISINFECTION for a guide to how much disinfectant to use when disinfecting a private well itself
    • Get the disinfectant into the water heater or water tank: Neat tip: if you are having trouble getting the bleach or disinfectant into your water heater, check out the water heater de-liming kits sold at plumbing suppliers as those often include a simple disposable pump that shoves the necessary chemical into the water heater tank through the heater drain valve. Alternatively you may need to remove a TPR valve and use that port to inject the disinfectant. If you remove a safety device such as a temperature and pressure relief valve be sure that a new one is installed properly, without leaks, and with a proper discharge tube. That same simple pump can push disinfectant into a water pressure tank or you may be able to inject it through an upstream water filter canister or for bladderless pressure tanks, through a tapping in the tank top or side.

      To get disinfectant or sanitizer into a water softener our brine tank sanitizing article (cited above) makes it easy to use a safe bleach solution that's introduced through the brine tank. But

      Watch out: some water treatment equipment such as the resin tank in a water softener may be damaged by disinfection or may may be difficult to flush-out after disinfection. For equipment that contains media (such as a water softener) or that may be impossible to drain directly, check with the equipment manufacturer about sanitizing procedures before trying the steps we outline below.
    • If your water equipment was contaminated by flooding see WELL DISINFECTION after a FLOOD as different stronger concentrations of disinfectant or sanitizer may be needed
    • Other water treatment equipment disinfectants, sanitizers and iron removal products are available; be sure to check with the manufacturer and to follow their instructions for these sanitizers or disinfectants as concentrations and procedures may vary.
  8. Wait 24 hours to give adequate contact time. To properly disinfect a water supply well, water tank, etc., you need both an adequate concentration of disinfectant and adequate contact time.
  9. Drain the disinfection or sanitizing solution from the tank of the water heater, softener brine tank, pressure tank etc. Typically you can use the tank or heater drain valve, connected through a garden hose to a suitable drainage location.
    • Watch out: It's best not to put high volumes of bleach-water into a private septic system as some septic systems such as aerobics and BAT designs may be damaged by too-high a bleach solution run through the system.
  10. Flush the tank with clean water until there is no "bleach odor"
    • Watch out: be sure that after sanitizing any water system or equipment that it is flushed thoroughly - until there is no odor or until a test shows no remaining disinfectant level (above what might be normally present in some drinking water disinfection systems).
  11. Restore all original fittings and return operating valves to their normal position
  12. Turn on the equipment: electrical controls & settings
    • Watch out: never turn on a water heater before it has been re-filled. Turning on an empty electric water heater will immediately destroy it. Turning on a gas or oil fired water heater that is empty may also damage the heater and risks fire or injury.

Water Equipment Disinfection Procedure Warnings - still more caveats

Water softener brine tank (C) Daniel Friedman

Well & Equipment Cleaning & Well Disinfection Procedures for Difficult Contamination Cases

This topic has been moved to a separate article found at WELL DISINFECTANT TABLE, POST FLOODING or select a topic from closely-related articles below, or see our complete INDEX to RELATED ARTICLES below.

Water & Water Equipment Disinfection Articles


Continue reading at WATER TREATMENT EQUIPMENT CHOICES - homeor select a topic from closely-related articles below, or see our complete INDEX to RELATED ARTICLES below.


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