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The exemption applications were for a Brooklands-Kainga residual disinfection exemption and a continuous monitoring and chlorine contact time exemption for the city's treatment plants and pump stations.
Council head of three waters Brent Smith said Taumata Arowai's decision was disappointing but expected.
“With this final decision, we’re in a better position to understand what would need to occur to be successful in any future applications,” Smith said.
Several factors led to the decisions, including a lack of a bacterial treatment barrier and an inadequate backflow prevention programme.
Taumata Arowai also declined the council’s application for an exemption from two rules relating to the chlorination of the city's supply.
One of the rules meant continuous equipment was needed to monitor chlorine levels at the pump stations, while the other aimed to ensure there was enough chlorine ‘contact time’ in the water to kill micro-organisms before it reached consumers.
The city council received draft versions of the decisions in May, indicating the applications would be declined.
The council then gave its feedback and Taumata Arowai’s final report took the feedback into account.
Taumata Arowai chief executive Allan Prangnell briefed city councillors on the decisions and indicated a willingness to explore solutions with council.
“Our exemptions process is new and the council was one of the first to make an application. The requirement for chlorine contact time is because some micro-organisms take time to kill.
"We suggested working together to get high quality research done into the aquifers that supply Christchurch’s drinking water to find out if these micro-organisms are in those deep, secure aquifers.
“We know Christchurch’s drinking water supply has characteristics that make it unlike other supplies, and the research would be of immense value and hopefully a way to resolve the issue.”
However, Smith said the complexities of the supply and the amount of investment required means getting a residual disinfection exemption will be a challenge.
“Smaller, less complex supplies, such as Brooklands/Kainga or Birdlings Flat, are more likely to be successful if we can adequately manage all the risks.”
The city council will prioritise the installation of continuous monitoring equipment and the replacement of the existing temporary chlorination system.