Lower Hutt's water supply will continue to be chlorinated while investigations into possible contamination continue.
A sample from a bore in Waterloo returned a positive result for E coli last week, the third positive result in five months.
The regional council has turned off public fountains in Lower Hutt and Petone as these can't be chlorinated.
Further water quality testing is also showing increasing amounts of bacteria.
Wellington Water said the cause of the positive E coli results was unclear and it may be related to the November earthquakes.
It said investigations into the source could take many months to complete.