The Blackwater River rises in the southwestern end of Canaan Valley in Tucker County at an elevation of 3,250 feet. Its flow is generally northeastward to its juncture with the Little Blackwater River and then southwestward to where it enters the Dry Fork of Cheat River near Hendricks, at an elevation of 1,705 feet. The Blackwater River is 31 miles long and drains an area of 142 square miles. In ascending order, its principal tributaries are Big and Tub runs, North Fork, Pendleton and Beaver creeks, Devils Run, Yellow Creek, Little Blackwater River, North Branch, Sand, Yoakum, Freeland, Club, and Mill runs. As it flows through Canaan Valley, the Blackwater meanders wildly and its flow is sluggish. Below Davis, the Blackwater River flows into Blackwater Falls State Park and drops 57 feet over the famous falls. It then begins a much straighter and more determined course as it carves out the picturesque Blackwater Canyon. Near the state park lodge, the canyon reaches a depth of 525 feet. The color of the Blackwater River is dark amber and is due largely to tannic acid from the abundance of hemlock and spruce trees in its drainage basin.

In April 2024, the Blackwater was named the 10th most-endangered river in the United States by American Rivers due to potential environmental damage from the construction of Corridor H through Tucker County.