The toilet tank has a lid that stops you from seeing inside. It's a good idea to lift it every so often and take a look because you might be surprised by what you see. The tank water can get dirty for several reasons, and the discoloration doesn't always transfer to the bowl.
Common sources of dirt in the toilet tank include minerals from the water supply, mold, algae and corrosion of plumbing pipes or metal parts in the tank itself. It's also possible that the water supply itself is tainted because of well problems or work being done on the municipal water system. If the supply is tainted, you'll also notice the discoloration at faucets.
Brown Water in the Toilet Tank
Iron in the water is the main reason for brown discoloration. It could be a sign that your old galvanized pipes are rusting, or it could mean that your water supply is rich in iron compounds. By itself, iron isn't a health problem, but it stains the sides of the tank as well as discolors the water. It also promotes the growth of bacteria.
You can handle a persistent problem with iron in the water supply by installing a water softening system. Iron is one of the minerals it removes. If the brown discoloration happens only in the toilet tank, it's a good idea to get a plumber to check the pipes supplying the bathroom. One or more of them may be corroded and need replacement.
The brown color in the toilet tank could be due to dissolved organic matter if you have a well. The discoloration may be accompanied by sediment, and the presence of either means that the well needs attention. The pump filter may need cleaning, or the well may have been breached, which can happen during storms or landscaping and construction projects.
Mold in the Toilet Tank
Because the toilet tank is covered, it's a perfect place for mold and algae to grow. These microorganisms may turn the water cloudy or give it a greenish tinge. Certain types of bacteria also grow in toilet tanks, particularly if the water is rich in iron. They are usually pink or white.
Treat all types of mold, algae and bacteria the same way. Empty the tank and (wearing gloves) wash down the sides and all the internal components with a disinfecting bathroom cleaner. Rinse the tank, let it dry out and then refill it and pour a cup or more of vinegar into the new water. Let the solution sit overnight before flushing.
Cloudy Water in the Bowl? Pour Vinegar in the Tank
When enough minerals dissolve in the water supply to turn the tank water cloudy, the cloudy water will pass into the bowl when you flush. This mineral-rich water can cause staining, and the minerals can collect in the flush valve opening and create a slow leak that causes the fill valve to cycle on and off.
Vinegar dissolves the salt deposits left behind by mineral-laden water. Empty the tank, pour in anywhere from a cup to a full gallon of vinegar and then let the tank refill. Give the vinegar several hours to work – or preferably overnight – before flushing.
When repeated every few months, the vinegar treatment will prevent cloudy water from causing problems. Vinegar also disinfects the water and is safer to use than blue disinfecting tablets. These tablets often contain bleach, and bleach corrodes the rubber gaskets in the fill and flush valves.
Chris Deziel is a contractor, builder and general fix-it pro who has been active in the construction trades for 40 years. He has degrees in science and humanities and years of teaching experience. An avid craftsman and musician, Deziel began writing on home improvement topics in 2010. He worked as an expert consultant with eHow Now and Pro Referral -- a Home Depot site. A DIYer by nature, Deziel regularly shares tips and tricks for a better home and garden at Hunker.com.