Three fire appliances were called to the Barry Ave complex in the centre of Cromwell just before 1am.
Cromwell Chief Fire Officer Steve Shaw said it took firefighters four hours to partially ventilate the complex and further ventilation continued throughout the day yesterday.
The fire was contained to the complex after starting near grating around the main swimming pool.
Mr Shaw said it took firefighters some time to locate the fire due to the thickness of smoke within the building.
It was easy to extinguish, but smoke damage would take "some time" to clean, he said.
"The entire inside of the complex is black."
The fire is not being treated as suspicious.
It is believed the cord of a pool suction system shorted, causing a fire which melted the plastic grating along one side of the six-lane lap pool inside the complex.
Central Otago District Council district aquatic centres manager Nicola Smith said the fire was "gutting" to pool staff and the community.
"It's such a great facility and everyone was so excited about it opening.
"At the end of the day you can't do anything about it but it's really disappointing," she said.
Insurance assessors started investigating the complex about 10am yesterday.
Mrs Smith said while structurally the building was fine, the entire complex would have to be cleaned from ceiling to floor.
"We'll have to empty the pools and start again. Soot is in every nook and cranny. Every crevice will have to be cleaned and it's going to be a big job," she said.
It was not yet known what, if any, equipment could be kept.
Mrs Smith said all office computers and cleaning devices were also clogged with soot.
"It's a major mess. At this stage we just don't know how much damage there is," she said.
Cromwell Community Board chairman Neil Gillespie said the fire was "soul destroying" to the people who worked hard to establish the complex.
"It's obviously a huge disappointment but on the positive side we should be grateful that it wasn't worse. We have to move on and try to get it up and running again as soon as possible," he said.
The complex was officially opened on May 1 after eight years of planning and fund-raising.
It comprises a six-lane, 2m deep lap pool, therapeutic pool, spa pool, and children's paddling pool.
Cromwell Swim Centre discount user cards will be accepted at the Molyneux Aquatic Centre in Alexandra.
Cromwell's new gym, NRG Health and Fitness, which is joined to the swim centre, was not damaged but closed yesterday.
It will reopen as usual from today.
