Stoney Creek is a small but viable salmon-bearing creek comprising over 4 km of watercourses along the main stem and four tributaries. Its upper reaches on Burnaby Mountain are fed by groundwater, rain and snow. The main stem has been channelized in places, forms a series of meanders in Stoney Creek Park, and then runs through an attractive ravine, eventually flowing into the Brunette River. Chum and coho salmon return to spawn every fall, and cutthroat and steelhead in winter and spring.

Stoney Creek is part of the Brunette watershed which also includes the following streams: Silver Creek, Eagle Creek, Beecher Creek, Still Creek, Massey Creek, Deer Creek and Beaver Creek. On Burnaby's south slope there is also Byrne Creek. Some of these have active streamkeeper groups. In addition, the Sapperton Fish and Game Club monitors conditions in the Brunette River and operates a breeding hatchery for salmonids.