The mother, whom the Otago Daily Times has chosen not to name, said the incident occurred on Sunday.
She said her son and daughter were in a changing cubicle and happened to look up see a man in the next door cubicle who had a mirror and a phone.
"He was next door in a room that was designated for schoolchildren.
"I don’t know if the man was recording what he was seeing on the mirror or what he was doing there, but it did worry me a lot."
She said the fact her children were unclothed and the man carried a mirror was "pretty disturbing".
She knocked on the door, approached the man and had a "bit of a tussle" with him as she tried to take the mirror and phone off him. Staff then intervened.
"The staff were very young. It was a bit of a confusing situation.
"It turned into a bit of a citizen’s arrest. The police came very quickly to the incident."
She hoped the Moana Pool staff had learned from the event, and developed protocol to avoid similar incidents happening in the future.
"Most of the lifeguards were very young, and it was not their fault at all. I hope they review things and make the right changes."
A Dunedin City Council spokesman said staff acted appropriately.
"Our staff acted immediately upon becoming aware of the incident at Moana Pool. Police were called and the person involved was spoken to and left with them.
"We’re reviewing existing arrangements to see if any improvements can be made, but we’re confident staff acted appropriately as soon as they were aware of the behaviour."
A man appeared in the Dunedin District Court yesterday charged with doing an indecent act. He was remanded on bail to reappear on December 3.