Heavy rain on Tuesday flooded the site for about 24 hours, extensively damaging the embankments and plant.
While the plant is still structurally intact, a large amount of tree debris, silt, gravel and floodwater has entered two treatment ponds.
Omakau couple Lloyd and Trish Harris, whose land borders the site, were concerned about untreated sewage from the plant discharging into the river and questioned the logic of having it situated close to the river where flooding was known to occur.
Repairs to the site by the Central Otago District Council as a result of previous flooding — including installation of new pond lining, security fencing and a treatment plant — had resulted in an $800,000 budget blowout and Mr Harris was upset ratepayers would be footing the bill for repairs that could have been avoided.
He felt the equipment for breaking down solid waste before it entered the treatment ponds should have been put in a concrete building to protect it.
"It should never have been designed like that.
"It should have been in a concrete block building so that nothing could get it.
"Why didn’t they just lift it all up and put it in a concrete drum so the river didn’t get into there," he said.
"I don’t know what damage is done to the gear. It might be savable, I don’t know, but really?"
The CODC said in a statement yesterday that while treatment was taking place, the flood had affected the performance of the ponds, resulting in a reduction in the quality of the discharge to the Manuherikia River.
People were advised to stay out of the river between Omakau and the Clutha River until further notice and any water taken downstream from Omakau for drinking should be boiled.
"During this period, the CODC will also be monitoring the water quality upstream and downstream of the site, once the river level drops to enable this to be safely undertaken," the statement said.
The council has been upgrading the site to improve the discharge quality during the past two years.
Three Waters director Julie Muir said it was "particularly distressing" to see the damage that had occurred to the new pond liner, and the equipment that had recently been installed on the site.
"This is the second time the site has flooded in five years.
"The first flood prompted a review of the long-term future of the site, given that increased frequency of flooding is expected in the future as a result of climate change."
A business case was being prepared to consider alternative options for treatment of wastewater from both Omakau and Alexandra.
It was considering options for treatment and discharge to land instead of waterways, she said.
