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Residents of Hawea and Arrowtown are being advised that their water will be chlorinated as of today.
In a statement, the Queenstown Lakes District Council said routine and unrelated testing showed elevated coliform counts this morning in both supplies, and emergency chlorination was being put in place.
Coliform bacteria are common in the environment (soil or vegetation) and are generally harmless; however, their presence does indicate the potential that more harmful pathogens could enter the system.
The chlorination was therefore a proactive measure, the QLDC said.
Chlorination would continue until tests showed the supplies are clear.
The QLDC said it would keep the communities informed.