It found 58-percent of pool filter samples taken from Atlanta-area pools in summer 2012 contained e. coli.
Researchers say it's likely this is a problem in public pools throughout the country.
The CDC suggests parents should take children to the bathroom every 60 minutes or check diapers every 30 to 60 minutes. Parents should also change diapers in a changing area not pool-side, they said.
ABC's Dr. Richard Besser says this may sound alarming but the study did not test for living bacteria and it's possible many of these germs were dead.
It is the reason why we put disinfectants such as chlorine in swimming pools in the first place, he said.