Lower Hutt's water supply could be chlorinated for months.

Water sourced from the Waiwhetu Aquifier has tested positive for E.coli bacteria for the third time since Kaikoura's earthquake.

Authorities have made the decision to chlorinate the water until they figure out why.

The public fountains at Buick Street in Petone and Dowse Square in central Lower Hutt have been closed because they can’t be chlorinated.

Greater Wellington Regional Council chair Chris Laidlaw said Kaikoura's earthquake could be responsible.

"An earthquake of that magnitude shifts a lot of material, it may well have have shifted something down underneath the aquifer itself."

Laidlaw said an investigation is underway, which includes looking into the November quake as the cause.

But he said the investigation could take months.

Meanwhile, Lower Hutt's mayor is assuring residents that the chlorination is just a precautionary approach.

"There's no need to boil it, it just simply means for those that may not have had chlorination before, it might be a slightly different smell, but it's not [an] unpleasant smell and it's quite safe to drink from the tap," Ray Wallace said.

Wallace said there are options for residents to subdue the smell of chlorine in the town's water.

"They can always fill the water from the tap and put it in a jug or bottle, put it in the fridge overnight, and that certainly takes away the chlorine smell."