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Emergency Disinfection of Cisterns and Other Rain-Catchment Systems

Floods and heavy rains can wash large amounts of debris and pollutants into cisterns and rain catchments systems, causing drinking water contamination. It is recommended to clean and disinfect your cistern following these events.

IMPORTANT: Water contaminated with fuel or toxic chemicals will not be made safe by disinfection. Do not enter the cistern. Gases and vapors can build up, creating a hazardous environment.


Cleaning the Cistern


  1. Clean the catchment area (for example, rooftop and gutters) and remove all debris.
  2. Remove all debris and water from the cistern.
  3. Scrub the inside with a stiff brush and a solution of 1 cup (about 0.25 liter) of unscented liquid household bleach (5%-6%) mixed with 10 gallons (about 38 liters) of water.
  4. Rinse cistern with clean, safe water, then drain.
  5. Refill the cistern with clean, safe water.

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Disinfecting the Cistern


  1. If the cistern is connected to any water treatment units, close valves to those units. Follow manufacturer recommendations for treatment system disinfection.
  2. Add 3 cups (a little less than 1 liter) of 5%-6% unscented liquid household bleach for every 100 gallons (about 380 liters) of water in the holding cistern. This should give you a chlorine concentration of about 100 parts per million (ppm). Table 1, below, shows cistern capacity volumes.

Table 1. Amount of Bleach to Add for Cistern Capacity
Cistern Capacity Unscented Household Bleach (5%-6%)
100 gallons 3 cups
200 gallons 6 cups
300 gallons 9 cups
400 gallons 12 cups
500 gallons 16 cups
If you do not know the cistern capacity, use one of the following formulas to determine the amount of water it will hold.

For a rectangular cistern:
  • Volume (gallons) = depth (ft) X length (ft) X width (ft) X 7.5.
  • Metric: Volume (liters) = depth (m) X length (m) X width (m) X 1,000.

For a round cistern:
  • Volume (gallons) = depth (ft) X [3.14 X radius squared (ft)] X 7.5.
  • Metric: Volume (liters) = depth (m) X [3.14 X radius squared (ft)] X 3,140.

Note: radius = half of cistern diameter.

  1. If the cistern is connected to interior plumbing, open each faucet and run the water until you smell chlorine (bleach).
  2. Turn off all faucets and allow the solution to remain in the cistern and plumbing for at least 12 hours.
  3. Drain all water from the cistern.
  4. Refill the cistern with safe drinking water.
  5. Open each faucet and run the water until you do not smell chlorine (bleach).
  6. Add 1 tablespoon of 5%-6% unscented liquid household bleach for every 100 gallons of water in your cistern to prevent microbial growth.

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Maintaining the Cistern


Maintaining water quality in cisterns can be difficult. Consider installing a treatment system to improve the quality and safety of cistern water. Contact your local health department or a water treatment specialist for more information.

Measure the chlorine residual regularly; chlorine test kits can be found at most swimming pool supply stores. Maintain a free chlorine residual between 0.2 ppm to 2.0 ppm to prevent microbial growth.

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