Your Water Could Contain Iron-related Bacteria: Iron bacteria are small organisms which naturally occur in soil and water. They are not known to cause disease, but can tint your water. This occurs when these bacteria combine iron and manganese with oxygen to form a yellowish, slimy buildup.Click to see full answer. Hereof, is it safe to drink yellow well water?Because yellow water is usually caused by iron or manganese concentrations, it is unpleasant but often safe to drink. Always contact your water provider and a plumber, however, to make sure that the issue is benign.Furthermore, what does it mean if my toilet water is yellow? If it is yellow, and your water source is well water, then it could be minerals. If city water, then it still could be pipe issue, or they have a problem in the lines, but, if it only happens at the toilet, and nowhere else, then it most likely is minerals. Flushing it a few times should clear it up. Beside above, what causes discolored well water? Even more obvious than odd noises in your plumbing system is the occurrence of strange odors, tastes, or murkiness in your well water. It could mean water levels have dropped too low or that dirt is in the pump. Causes of Discoloration in Water: Reddish/brown: Iron or manganese.What causes iron bacteria in well water?Iron bacteria are small living organisms that naturally occur in soil, shallow groundwater, and surface waters. These bacteria combine iron (or manganese) and oxygen to form deposits of “rust,” bacterial cells, and a slimy material that sticks the bacteria to well pipes, pumps, and plumbing fixtures.