The Blackwater River is formed at Cilleyville,[2] a village in the western part of the town of Andover, by the junction of two branch streams.

Cascade Brook, the western branch, begins at Cascade Marsh in the northeast part of Sutton and flows northeast to Wilmot Flat, where it is joined by the outlet of Pleasant Lake of New London before continuing east to Cilleyville.

From its start at Cilleyville, the Blackwater River flows east through the town of Andover, passing the village of Potter Place.

Beyond Andover village, the river continues to wind its way east, eventually turning south near the Blackwater Bays and dropping over rapids through the village of West Salisbury to the impoundment area of the Blackwater Dam in the town of Webster.

Below the reservoir dam, the Blackwater encounters a short, intense whitewater stretch before flattening again for the final miles to the Contoocook in Hopkinton.