Symptoms: Rusty, brown, or yellow water appearing in the hot water.
Cause: Complaints of discolored water are commonly blamed on water heaters, but in fact it is a rare occurance for today's high quality glass lined tanks to have a lining failure significant enough to allow water to contact enough bare metal to discolor the contents of even a small tank. The most common cause of "rusty" water is a non-toxic iron reducing bacteria, scientifically termed Crenothrix, Leptothrix, and Gallionella. Iron Bacteria is commonly found in soil, water wells, water treatment plants and water distribution piping systems where soluable iron exceeds 0.2 ppm, higher levels make conditions even more favorable. Soluable iron in the water provides food for the bacteria. Rusty discolored water is the end result of the bacteria feeding process. Water heaters and storage tanks usually require new anode rods as presence of iron bacteria contributes to premature anode failure.
Treatment: The simplist treatment avaiable is shock-chlorination of the system. This is a surface treatment, and often requires repeated trials in heavily infected systems. The cholorination of a system requires that you follow each step explicity to avoid an un-treated portion of the piping system from reinfecting another part.
Since rusty water is caused by a bacteria presence and is not caused by the water heater, any treatment would not be considered warranty related.