Stagnant water has little dissolved oxygen in it and is a prime breeding ground for bacteria. Pools of water, such as those sitting in the back of an infrequently flushed toilet tank, become stagnant as the oxygen works its way out of the water and is not replaced. The only way to prevent water from becoming stagnant is to aerate it. This can be accomplished through good water circulation.
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Don rubber gloves to protect your hands from contamination. Exposure to stagnant water is a health hazard, and rubber gloves will protect your skin from absorbing any germs or bacteria living in stagnant water.
Lift the lid of the toilet tank to ensure there is no mold present. According to the website Allergy Nursing, the presence of mold is often a sign of stagnant water. Remove mold immediately by pouring 2 cups of bleach into the tank to preserve the health of those around the toilet. Leave the bleach to sit for at least 15 minutes, then flush.
Flush the toilet and wait for the tank to refill with fresh water. The water level in the toilet bowl will drop, then rise to its normal level before the tank is filled. Once the tank is refilled, flush the toilet again. Repeated flushing will rid the pipes of stagnant water.
Flush the toilet at least once every three days to prevent water from becoming stagnant.