The Kokoda and Long Tan Pools have been closed after routine testing detected bacteria in the water.
Townsville City Council conducted its fortnightly testing of the water quality at all pools which showed E. coli as being present at Kokoda and Long Tan.
The pools have been closed for further testing and treatment and are expected to be reopened before the end of the week, in time for the school holidays.
Any visitors to these pools that begin to feel unwell should seek medical treatment. Symptoms typically begin three to four days after exposure.
The Northern Beaches Pool is still open to the public.