Problems With Cistern Water in Your Home

Updated February 21, 2017

Cisterns have become an excellent water saving device in warm climates with limited rainfall. The home is set up with a cistern that collects water runoff from the roof. Unless you have a specialised treatment system, the water is nonpotable and is used primarily for gardens and flushing toilets. A cistern can be above ground or buried and can be as simple as a rain barrel. Water problems in the home are most often noticed in the bathroom where the water is used to fill the toilet tank reservoir. Cisterns that deliver drinking water are rare and must have extensive filtration systems and chlorine pumps and be tested frequently for bacteria and contaminants.

No Water

The lack of water in the home is usually due to the lack of rain. Rain is collected from the roof and filtered into the cistern. A drought period means that the cistern is not getting refilled, but the use is probably higher. If there is plenty of water in the cistern, water problems in toilets might be due to a faulty ballcock in the tank. No water from the tap could mean a leak or breakdown somewhere in the pipes. The cistern could also need larger pipes for water delivery. Friction causes pressure loss in a pipe, but there is less friction in a larger pipe.

Odour and Discoloration

Foul odour and yellow or brown water is a common problem when using a cistern for indoor water. The cause is a dirty tank, a broken chlorine pump, introduction of a contaminant or even just a dirty roof or downspouts. The cistern should be cleaned annually to prevent build-up of debris. Some tanks have a sediment catcher, which can become over full and will need to be replaced or cleaned. The cistern should have a properly fitted lid and no gaps where an animal or contaminant can be introduced. An aquarium pump or something similar will cause water movement that will deter the formation of algae and some bacteria.


Mosquitoes are not necessarily a problem indoors, but you may have to treat the cistern if you develop a mosquito problem in the containment unit, which means your treated potable water will not be usable. The method of treatment is with Bacillus thuringiensis, which is a naturally occurring biological agent. The bacteria comes in a floating cake that you put into the water. Mosquito larva live in stagnant water, so the aquarium pump is a good deterrent to these pests.


At least once annually, the cistern should be cleaned out. The sides need to be scrubbed with a stiff brush. Some people advocate the addition of 1/4 cup of chlorine bleach for every 10 gallons of water. If there is a sediment trap, such as a sand filter, the top 1 to 2 inches of sand need to be replaced. The roof and gutters should be kept clean and free of debris. Any screens or drainage holes need to be inspected and freed of dirt and objects.

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About the Author

Bonnie Grant began writing professionally in 1990. She has been published on various websites, specializing in garden-related instructional articles. Grant recently earned a Bachelor of Arts in business management with a hospitality focus from South Seattle Community College.