While not a common occurrence, it certainly is disconcerting to turn on the hot water faucet and see brown water coming out -- particularly if you happen to be in the tub or the shower at the time. There are two main reasons for brown water. One may lie with the water heater itself while the other may be an actual problem with either the household water supply or the water pipes. Troubleshooting your water heater will help you narrow down the culprit.
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Turn on the cold water faucets. To ensure that the problem is not with the household water supply or the pipes, run cold water only in your sink. If you do not notice any brown water, this is an indication that the problem is indeed with your water heater.
Turn off the power and water supply to the water heater. If you have a gas water heater, extinguish the pilot light according to the manufacturer's instructions. You do not want the power supply or gas on while you are working around the water heater. Twist the water supply valve to the "Off" position.
Drain out the water in the heater. You can do this with buckets or, ideally, hook a hose up to the output valve on the water heater and run it into the nearest drain (make sure the hose is going downhill). Completely drain out all of the water.
Flush the water heater. Brown water is typically caused by a buildup of iron-rich sediment in the bottom of the heater. Turn the cold water on and run the water through the heater. Keep the hose attached to the output valve and run the water through it. You may need to repeat this step until the water coming out of the heater is clear.
Turn the heater back on and restore the water supply. Turn on the power to the water heater or light the pilot light. If you have never lit a water heater pilot light before, you may want to ask your local gas company to send someone out to light it for you. Turn the water supply back to the "On" position.