A thorough shock chlorination of the well and water system may destroy all iron bacteria colonies. In this situation you will need to repeat chlorination treatment periodically. Other nuisance organisms include slime bacteria and sulfate reducing bacteria which produce a rotten-egg odor. Chlorination will kill or control these bacteria. Nuisance bacteria do not cause disease.
Chlorine helps remove manganese and hydrogen sulfide in the same way.
Chlorine will not remove nitrates from water. The claims of some water treatment firms imply that nitrates can be removed by chlorination. This is not true. However, if the concentration is great enough the water will taste bad so consumption may be reduced. In those cases an activated carbon or charcoal filter may be used to remove the chlorine from the drinking water.