Rust in well water can come from iron or manganese deposits that mix with the air, also known as iron bacteria. The bacteria can grow into a slimy material that sticks to well pipes. This can cause the water to change color, have a strange taste or odor.
Although it is unknown if iron bacteria can cause disease, it can create a good environment for other harmful bacteria to grow. When repairing pumps, well pipes and well equipment, they should be disinfected properly. A laboratory can test the water if there is any indication that the well water is contaminated.