Disinfecting Your Water System

What is Disinfection?

Disinfection is the process by which chlorine is added to a water system in large amounts to kill bacteria and to burn up organic materials which serve as food for bacteria.

When does a water system need disinfection?

  • After construction of a new water supply.
  • After making repairs to an existing water supply.
  • After a water system has been unused for several months.
  • When the results of a coliform bacteria test indicate contamination.
  • Sometimes disinfection will give relief from iron bacteria and from sulfide odors caused by sulfate-reducing bacteria often associated with iron bacteria.

How is a water system disinfected?

1) Pour household bleach (Clorox, Purex, etc.) into the well, spring, or storage tank, and mix thoroughly if possible.

For most water systems, a gallon of bleach is more than adequate. For systems with large storage tanks, use an extra gallon for each 1,000 gallons of storage capacity. Use bleach with no additives such as scents. Chlorinated well water can be circulated by pumping it through a hose and discharging it back into the well.  This serves to clean parts of the well above the water line, as well as to aid in mixing.

2) Pump the chlorinated water through the entire system.

Do this by opening each tap until you can smell the chlorine coming through. Shut off the tap and go on to the next one.  Leaving a line un-chlorinated can cause recontamination of a system, so be sure to open every tap, including hot water and irrigation taps.

3) Allow the chlorinated water to stand at least overnight. Flush out the system until the chlorine is gone.

This can take several hours and it can be difficult to determine if all of the chlorine has been removed. The best results are obtained with a chlorine test kit, like a swimming pool test kit (chlorine testing materials are also available at the lab for a nominal charge). As far as possible, do not flush highly chlorinated water into a septic system, as the chlorine may have an adverse effect on the bacteria that make septic systems work.  Do not use highly chlorinated water for irrigation purposes or for drinking.  Once the odor of chlorine has become very faint there is no harm in using the water as usual.

4) Take a sample in a laboratory-sterilized bottle for coliform bacteria analysis.

Do this only after all chlorine has been flushed from the system or the sample will be invalid. It is highly recommended to wait a few days after all the chlorine has been pumped out of the system before you collect a sample.  Health department guidelines require that two successive repeat samples be coliform-free before the water source can be considered safe. This is because it often takes some time for bacterial contamination to reappear in a disinfected water system. Sampling again during the rainy season, when contamination is most likely to occur, is also recommended.

5) If test results continue to show contamination, you have several choices:

  • Look again for possible sources of contamination, fix them, and re-sterilize the system as above. Occasionally repeated sterilizations do remedy the problem if bacteria are protected from the chlorine by large amounts of organic matter, like wood, dead animals, bacterial slimes, algae, etc.
  • Install an approved chlorination system to continually disinfect the water. These require meticulous maintenance and may not be approved by your local health department (check with them for current regulations).
  • Use the contaminated supply for irrigation only and hook the domestic system up to a coliform-free water supply, such as a new well or a public water system.
  • Sometimes surface water contamination can be eliminated in a well by lining the casing and resealing it.  Check with a well drilling or service company for further information.

Attention: open in a new window. PDFPrintE-mail