The pool was closed on Tuesday following damage to pipes caused by an electrical fault.
Dunedin City Council parks and recreation planning manager Jendi Paterson said it re-opened at 2pm today, but had to be closed about an hour later due to a mechanical problem related to the earlier fault.
"It wasn't until the water had filtered through the pool for some time that the issue with the strainer became apparent," she said.
The fault meant the water in the pool could not be filtered properly.
The repair work would be done as soon as possible, Ms Paterson said.
In the meantime, there were three other pools which were open: Moana, Mosgiel and Port Chalmers.
While the St Clair pool was unavailable, swimmers with St Clair memberships could use them at any of the other pools.
