The Stony Brook starts at 40°39′12″N74°27′11″W / 40.65333°N 74.45306°W / 40.65333; -74.45306, near the intersection of Hillcrest Road and I-78. It flows southeast, crossing Stirling Road, before turning southwest. It then turns northeast and flows into Watchung Lake. In Watchung Lake, it joins an unnamed tributary from the northeast and another one from the southwest. It then leaves the lake and goes southeast through the town of Watchung. It passes through the Stony Brook Gorge in the first Watchung Mountain and over the Wetumpka Falls.