Bouchard, of North Bay, Ont., was sixth at the halfway mark but roared to the finish with the fastest split on the last length for the win in two minutes 10.02 seconds.
She upset American Elizabeth Beisel, the bronze medallist at the 2012 London Olympics, who was second in 2:10.09. Taylor Ruck, a Canadian living in Arizona, was third in 2:10.22.
The UBC Thunderbirds were also victorious, placing first in the men's 4 x 200m freestyle with Marshal Parker, Keegan Zanatta, Yuri Kisil and Stefan Milosevic. The University of Alberta was third with Hunter Balch, Evan Letkeman, Joe Byram and Connor Bayne.