The Holly River begins as two separate streams—the Left Fork and the Right Fork—in the rugged mountains of Webster and Randolph counties. These two streams join together in Braxton County.

The main Holly River is actually the shortest river in West Virginia, flowing just over three miles before it enters Sutton Lake. Before the dam created the lake, the Holly River flowed into the Elk River. The two forks and the main river drain an area of 148 square miles, the largest watershed of any of the Elk's tributaries.

The Left Fork, known for being a great trout stream, runs through a corner of Holly River State Park. The river basin was once a major area for logging, with railroads built up both forks in the early 1900s to carry timber to the large sawmill at its mouth.