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The pool was scheduled to open today.
Dunedin City Council aquatic services team leader Heath Ellis said he was confident the clean-up would not take too long.
"We were all ready for the October 1 opening, but the high winds have caused some flooding. We will advise the new opening date as soon as possible."
The pool will be open weekdays from 6am to 7pm and weekends 7am to 7pm, until March 31.