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The building of a stopbank, which will be 700m long when completed, began in the last week of February.
Clutha District Council water services manager Hank Stocker said the aim of the new infrastructure was drainage improvement, rather than protecting Milton from river flooding.
The flood bank had been built to prevent the river from flowing back into the drainage area, Mr Stocker said.
Manager district assets Jules Witt said the pump station, which was yet to be built, would boost the capacity of the existing drainage system by emptying the outlet ends of the drains, even when the river was high.
"The flood bank will prevent river water from entering drains, while also protecting some low-lying properties," Mr Witt said.
Once the pump station was constructed, it would be able to pump 1200 litres of water per minute at its peak, Mr Stocker said.
"Peak capacity may be once every 50 years."
The project had been discussed for a long time, because Milton had a history of surface flooding, with significant flooding in April 2006 and August 2007, Mr Stocker said.
The contract for construction of the storm water drainage system was awarded to Waihola Excavation for $777,705.
Council expects the project to be completed by winter.