As a result the pool was closed yesterday and will remain so until the seas die down, which was in the "lap of the gods", Dunedin City Council aquatic services manager Steve Prescott said.
High waves crashing over the walls around the facility had filled the pool with mud, sand and debris requiring it to be pumped out, he said.
The waves had also broken seating, dislodged tiles and ripped covers causing about $3000 to $4000 damage.
It was the first time such damage had happened to the pool since it was redeveloped about four years ago, Mr Prescott said.
During the redevelopment walls were raised around the pool and wave-breaking stones placed around its edge.
"It used to happen all the time before the redevelopment."
There was nothing further that could be done to prevent the inundation from occurring again and was something that went with having a facility so close to the sea, he said.
"It's just nature taking its course. There is nothing we can do about it."
The council would be watching the tides and wave heights closely during the next few days, before deciding to reopen the facility, he said.
The pool cafe remains open.
