Stony Brook
- Flat Brook
- Guangfo Line
- Ludlow, Massachusetts
- Shixi station
- Stoney Brook Township, St. Louis County, Minnesota
- Stony Brook (Charles River tributary, Boston)
- Stony Brook (Charles River tributary, Weston)
- Stony Brook (Delaware River)
- Stony Brook (Fishing Creek tributary)
- Stony Brook (Green Brook)
- Stony Brook (Mehoopany Creek)
- Stony Brook (Merrimack River tributary)
- Stony Brook (Millstone River)
- Stony Brook (Schoharie Creek tributary)
- Stony Brook (Souhegan River tributary)
- Stony Brook Air Force Station
- Stony Brook Meeting House and Cemetery
- Stony Brook Power Plant
- Stony Brook Reservation
- Stony Brook Seawolves
- Stony Brook State Park
- Stony Brook University
- Stony Brook University Hospital
- Stony Brook Wildlife Sanctuary
- Stony Brook station (Boston and Maine Railroad)
- Stony Brook station (LIRR)
- Stony Brook station (MBTA)
- Stony Brook, New York
- The Stony Brook School