Iron in your water can cause stains that are yellow, orange or even a red coloration. The Environmental Protection Agency (EPA) sets the maximum contaminant level (MCL) for substances in household water. For iron the MCL is .3 parts per million; if your iron level is above the MCL you may experience staining or your water may have an unpleasant taste.
There are multiple forms of iron, and treatment methods are dependent upon the form of iron you have. Ferric iron is insoluble and comes out of the tap discolored; ferrous iron is soluble and comes out of the tap clear. When exposed to oxygen or other oxidants (such as hydrogen peroxide or chlorine bleach) ferrous iron is oxidized. Both forms of iron can cause staining that is unpleasant to live with and can make it difficult to keep toilets and sinks clean. It can also stain laundry and the inside of your washing machine.
Pink staining is caused by airborne bacteria or in some cases manganese. If you have pink staining it is most likely the result of little or no chlorine, allowing airborne bacteria to develop. If this occurs primarily in your toilet you may want to add a small amount of bleach to the toilet. Manganese primarily results in a brown or black coloration but in rare instances may cause a pink coloration as well. The EPA has set a level of .05 parts per million (ppm) for manganese; it is considered non-toxic, however in levels over .5ppm can cause diarrhea or upset stomach.
Tannins are caused by decayed vegetation and cause tea-colored staining, or brown streaks. There are over 12,000 types of tannins and they can produce staining similar to manganese, so tannins are often misdiagnosed.
Black staining can be caused by iron sulfides which are formed when iron combines with sulfates. (If you have black stains and a sulfur smell this is the likely culprit.) It can also be caused by high concentrations of manganese and/or manganese sulfides.
If your pH is too low, it becomes acidic and can cause blue staining and pinhole leaks in copper pipes. On the other hand if your water is high in pH and total dissolved solids it can also cause blue discoloration.