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Because chlorine that is initially used to disinfect our water actually poses one of the biggest potential health hazards.
Yes Chlorine kills germs in the water supply. But, it cannot kill all pathogens. Bacteria responsible for diarreah will not die quickly. It needs days of exposure to chlorine and hence simple treatment will not kill this bacteria.
But, Chlorine is also a dangerous for our health if not controlled to the extent allowed. Using RO system to remove the chlorines may help to make drinking water more safe.