Trudeau thanked emergency responders, civic leaders and volunteers for helping deal with the situation.
He said the community showed real resilience.
The prime minister also praised members of the Canadian Armed Forces for helping flooded areas.
Bracebridge, more than two hours north of Toronto was flooded in 2013, but this year was far worse.
Trudeau also warned that more extreme weather events will occur in future as the climate changes.
WATCH: Bracebridge homeowner talks about flooding impact (May 1)