The Riverway Pool has been closed after testing detected bacteria in the water.
The bacteria were discovered following routine testing of the pools conducted by Townsville City Council.
The closure applies to the Upper and Lower Lagoon and to the toddler pool as they all share the same filtration system.
Council is now undertaking the treatment process and the pool will remain closed until the water levels are safe.
There have been no reports of illness by the community.
Council advises any residents that have visited the pools recently and are feeling unwell to visit a doctor.