Pequawket Brook rises in the town of Madison, New Hampshire, near a low height of land north of Silver Lake. The brook flows north past extensive sand and gravel excavations to Conway, where it enters Pequawket Pond, a natural pond that has been enlarged by an impoundment in the center of Conway village. Below the pond dam, the brook flows north for one-half mile to the Swift River, just one-half mile above the confluence with the Saco River.
New Hampshire Route 113 follows the brook in northern Madison. NH-16 follows the brook from NH-113 to Conway village.
The Conway Branch rail line follows the brook and ponds.