The Warriors have two sites used for varsity athletics; The Physical Activities Complex (PAC) located on the main campus is the site of the Carl Totzke Court, which is used primarily for basketball, while the Columbia Ice Field (CIF) complex on the north campus houses the Columbia Icefield Arena for Ice hockey, as well as Warrior Field on the opposite end, which has been the home of Warriors football since 2011.

Prior to 2011 the Warriors football team shared University Stadium with the nearby Wilfrid Laurier Golden Hawks.

The stadium was later sold by the City of Waterloo to Wilfrid Laurier University in 1992, where it is now the home of the Golden Hawks.

The Waterloo Warriors football team has been in operation since 1957, winning two Yates Cup conference championships in 1997 and 1999.

The team dominated the OUAA in the early 1970s, and a defining moment of the program was the 1975 CIAU final against the Manitoba Bisons, where in the last seconds of play, forward Phil Goggins made two consecutive shots to bring the Warriors to an 80–79 victory, which won them the championship.

Prior to the 1997–98 season, they competed in the Ontario Women's Interuniversity Athletic Association (OWIAA), until their merger with the OUA.

Club teams include ringette, women's football, rowing, dragon boat, ball hockey, lifesaving, and artistic swimming, among others.