The brown stain is probably from a large amount of iron in your water. If you have ever drunk water containing a bit of iron in it, you would know from the metallic taste left in your mouth that dissolved chemicals in drinking water can be less than desirable. Color in drinking water can be caused by dissolved and suspended materials, but most often comes from rust in the water pipes.
Although water can contain contaminants, which are usually removed by water-supply systems, the plus side is that the water you drink likely contains a number of dissolved minerals that are beneficial for human health. And, if you have even drunk "pure" water, such as distilled or deioninzed water, you would have noticed that it tasted "flat". Most people prefer water with dissolved minerals, although they still want it to be clear.
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