Cory McLean said his daughter felt "embarrassed" and "nervous" after the incident.
"To be honest, I was so surprised by the actual rule when I heard about it that I thought for sure it was some sort of mistake, some rule from way back that just got carried into the present," said McLean, who described the policy as "sexist and antiquated."
In the city's 2015 Community Guide, the policy states that "females ages four and older must wear a bathing top in … enclosed or fenced pools."
The city said it would review the section of the swimming attire policy related to tops and that during this review the requirement would not be enforced.
McLean said he is confident that permanent change is coming.
"I would like to see some gender equality in the rule, that's all. We were never trying to announce that we want small children to be topless, running around in parks," said McLean.
"We're not exhibitionists, we're just people that noticed a little bit of a loophole in the rules and guidelines that caused the gender inequality and we just wanted to make everyone aware of it."
In a press release, the city apologized "that the event caused the little girl to feel singled out or embarrassed," adding that the lifeguard who issued the command was following city policy.
"We've received a lot of diverse feedback about the part of the policy that requires girls above the age of four to wear a swimming top," said Kristene Scott, general manager of parks and recreation, in the release.
"Some people support the policy while others feel it no longer meets their needs. The city's challenge is to find a reasonable balance that serves our community."
Councillor says rules must apply equally
Ward 6 Coun. Mark MacKinnon says the city should not have a rule that prevents women, but not men, from going topless.
"We need to have a policy that has been updated for case law," MacKinnon said, referring to the Gwen Jacob's case, in which women won the right to go topless in public.
"In terms of toplessness, it just makes sense to remove that guidance completely. It's not age related. It's gender related."
MacKinnon said changing the rules to allow women to go topless at city pools would align Guelph with neighbouring communities like Cambridge.
Citizens of Guelph are encouraged to take part in the city's review of its swimming attire policy.
The city says details on how that can be done will be released in the coming weeks.