Water Polo began at Churchie in 1996 fielding seven teams from Years 7 to Year 12. It gained a popular following and was offered as a school sport, and in 1997 entered its first competition with five teams. Training is held in the 25 m pool each Tuesday and Thursday mornings during Term 2 and games are played on Friday afternoons at the All Hallows pool in Fortitude Valley. A significant number of students have been selected to represent teams at regional, state and national levels. Churchie won the 2003 Southern Skies Open Championships and the 2012 Queensland Schools Tournament, and was runner-up in the 2004 Tasman Cup Tournament.
Even though Water Polo is not a GPS competition, in 2009 and 2010 the team emerged as undefeated Premiers in the Independent School Competition.
Churchie students who have represented Australia at various levels include William Armstrong, James Broadley, Michael Dance, Tim Dance, Nick Godfrey, Duncan Greenbank, Stewart Greenbank, Zac Hudson, Tyler Sinclair, Tom Woudwyk and Alex Yeates.