The most common cause of brown well water is iron contamination. A sudden change in water color means that the contaminant is newly introduced to the well, and it may be caused by industrial contamination, rusty plumbing fixtures or natural iron leaching from the ground.
Chemical treatment and sediment filtration are used to remove iron from well water. After the iron has been removed, the water requires further chemical treatment to kill any iron-consuming bacteria that may have formed a biofilm in the well water. If iron remains in the well water, the bacteria can return and cause problems to recur.