Artesian water wells in Lower Hutt have been closed and the city's water supply will continue to be chlorinated while officials investigate increased bacterial activity.
November's Kaikoura earthquake has been identified as a possible cause for the problem.
The fountains in Petone's Buick Street and Dowse Square - popular spots for locals to collect untreated water - are closed as a precaution because they cannot be chlorinated.
Officials are playing down the risk to the public and say tap water is still safe to drink.
They have been chlorinating the water supply since positive E.coli tests in the Waiwhetu aquifer from last week.
The most recent positive test came from the Waterloo well last week and monitoring showed an increasing amount of bacteria activity across the aquifer.
People valued their untreated water supply but public safety is the number one priority, Lower Hutt Mayor Ray Wallace says.
Wellington Water acting chief executive Mark Kinvig says they don't know why bacterial activity has increased.
"It may be related to the November 2016 earthquake. We're carrying out investigations into the source but this is expected to take many months to complete."
The water supply company will be looking at non-chemical treatment options that will allow the public fountains to be reopened.
About 70,000 Lower Hutt customers usually receive an unchlorinated water supply and around 330,000 customers in Wellington, Porirua and Upper Hutt get chlorinated water.