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Otago Regional Council engineering manager Michelle Mifflin said Brighton was badly affected when water reached the local store and began flooding the camping ground, where people were on Covid-19 lockdown.
The storm surges also affected nearby Taylors Creek, as well as Long Beach and Waikouaiti, north of Dunedin.
The Clutha River mouths were not affected as the high volume of water flowing flushed out sandbar build-up.
Ms Mifflin said quick action had been required last week to clear the affected river mouths.
Brighton escaped damage after the community, police and Fire and Emergency New Zealand provided sandbagging to stop the flooding.
"ORC engineering staff monitored the high tides during the night until they receded, and then assessed what could be done during the day to enable built-up water to release back into the sea."
"There are a number of risks if these mouths don’t freely allow water out to sea, which is why this work is considered essential.
"Excess water can cause erosion, it can flood estuaries and lagoons and it can threaten communities in some instances, as we saw last week.
"There’s also a wider environmental and social impact that coastal flooding can have on beaches and coastal habitats."
The river mouths were now functioning normally, but staff would keep a close eye on them, she said.