Stony Creek is situated in the upper part of the Memramcook River Watershed. The Stony Creek sub-watershed has an area of approximately 25 km².
Near its mouth, the physical habitat of Stony Creek is characterized by the presence of mud and silt on the bank and bed of the watercourse. In this portion, the environing region of Stony Creek is mainly open and is made up of high grasses.
Near the railroad, there is presence of erosion on the true right bank. Sediment in great quantity is also noticed. Passed the TransCanada Highway, the physical habitat of Stony Creek improves considerably and the substrate is made up of gravel and rocks. In this portion of the watercourse, the surrounding area is mainly wooded.