| Stony Brook | |
| Pushpin Map: | New Hampshire#USA |
| Pushpin Map Size: | 250 px |
| Subdivision Type1: | Country |
| Subdivision Name1: | United States |
| Subdivision Type2: | State |
| Subdivision Name2: | New Hampshire |
| Subdivision Type3: | County |
| Subdivision Name3: | Hillsborough |
| Subdivision Type4: | Towns |
| Subdivision Name4: | Greenfield, Lyndeborough, Wilton |
| Length: | 10.6miles |
| Source1: | Lyndeborough Mountain |
| Source1 Location: | Lyndeborough |
| Source1 Coordinates: | 42.9206°N -71.8053°W |
| Source1 Elevation: | 1270feet |
| Mouth: | Souhegan River |
| Mouth Location: | Wilton |
| Mouth Coordinates: | 42.8442°N -71.7389°W |
| Mouth Elevation: | 338feet |
Stony Brook is a 10.6adj=midNaNadj=mid[1] river located in southern New Hampshire in the United States. It is a tributary of the Souhegan River, which flows to the Merrimack River and ultimately to the Gulf of Maine.
Stony Brook rises in the town of Lyndeborough, New Hampshire, in a valley between Lyndeborough Mountain to the north and Winn Mountain to the south. It flows west into the town of Greenfield, then turns southeast and reenters Lyndeborough, continuing to the Souhegan in the mill town of Wilton.
It is paralleled from Greenfield to Wilton by New Hampshire Route 31 and by the former Hillsboro Branch of the Boston and Maine Railroad.