Despite a months-long investigation, no definitive conclusions have been reached on the source of the contamination.
Mayor Ray Wallace said he supported the decision because a situation like the gastroenteritis outbreak in Havelock North could not be repeated.
"Three people lost their lives, sadly as a result of a contaminated water supply. We can never ever allow that to happen again."
Wallace said it was still a sad day because residents had enjoyed unchlorinated water for decades but public safety was paramount.
"It is quite clear from the evidence that safety of the water supply cannot be guaranteed anymore without chlorination."
Lower Hutt woman Hayley Smith said her family had already looked into getting a filter unit for their home.
She said even her 10-year-old son had noticed a difference in the water since chlorination began.
"The other day when I asked him to go and get a drink of water he said to me 'I don't like our water anymore mum', and I've noticed both the kids are drinking a lot less water than they were before."
Smith said if they chose to have the system installed, it would filter water as it entered the house.
"We have also noticed the baths are a lot stronger smelling and the shower water is not as good as quality as it used to be, or it doesn't seem to be."
Greater Wellington Regional Council environment regulatory manager Al Cross said an investigation would continue into the source of the supply's contamination.
"We may not ever really get a full grip of the pinpoint source. It would be fair to say that's a big ask, but the most important thing is that we do the work to do our best to understand it and we safeguard the system for the future."
Wellington Water estimated it would initially cost about $5 million to install the necessary treatments at the Waterloo plant in time to meet this summer's water demand.
Additional operational costs would be about $1.5 million for things like power, chlorine, the regional safety water plan and staff resources. Annual operational costs would then be about $875,000.
Artesian water wells in Petone and Dowse Square remain chlorine-free and are only being treated with UV.