There are several possible reasons for discolored water, but ultimately water testing will be critical in diagnosing the cause of the problem. Minerals, including iron and magnesium, algae, pipe degradation and resin beads can all cause black water.
Magnesium is often found in water and when mixed with oxygen, turns black. If you look in your toilet tank and the inside is black, then you have magnesium and probably iron in the water. In either case, they are harmless to you. But if you want them gone, you will have to filter your water. Call a water softener company to analyze your water and determine what you need to remove the color. If the piping in your house is steel or galvanized, you could be getting mineral flakes from exposed iron (rust). Under the right conditions, with the right natural minerals and elements in the water (like magnesium), then you could get black water out of the faucets. Natural resin beads from your water softener are often black in color, like charcoal. Sometimes the water softener can break down and the resin beads can get our and into the water system. Roto-Rooter can properly diagnose the problem and offer some solutions.