[1] The Stony Brook starts at 40°39′12″N 74°27′11″W / 40.65333°N 74.45306°W / 40.65333; -74.45306 just outside of Watchung, New Jersey, near the intersection of Hillcrest Road and I-78.

It flows southeast, crossing Stirling Road, before turning southwest.

In Watchung Lake, it joins an unnamed tributary from the northeast and another one from the southwest.

It passes through the Stony Brook Gorge in the first Watchung Mountain and over the Wetumpka Falls.

Entering North Plainfield, New Jersey, it crosses Route 22 and joins the Crab Brook.