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The treatment itself can be harmful. Too much fluorine and chlorine come to mind. Although small amounts of fluorine is obviously good for you. On the other hand, a lack of natural minerals can have long term negative effects in a human if distilled water was ALL the human drank. Natural water has magnesium, potassium, calcium in small amounts and obviously these are essential for us.
That is all I can think of. Is this really an engineering problem? :) Seems more like a biology class.
chlorine as a disinfectant forms HAAs and THMs, ozone forms bromate as by-products, chloramine forms dichloroamine and trichloroamine, chlorine dioxide forms chlorites and chlorates. and so on. these by-products are harmful to human health.