Holly River begins as two separate forks in the rugged mountains of Webster and Randolph counties in West Virginia. These forks flow westward, coming together in Braxton County to form the Holly River mainstream just before the river enters Sutton Lake. The two forks and the main river drain an area of 148 square miles, the largest watershed of any of Elk River's tributaries.

The Left Fork of Holly, 25.1 miles long, is a popular trout stream. It originates in Randolph County two miles southwest of Pickens and flows through a corner of Holly River State Park. A well-known feature of the Left Fork is "Shupe's Chute," a curving, natural water slide carved into the rock on Fall Run, where the run enters the Left Fork. It was named for Walt Shupe, who was superintendent of the state park from 1966 to 1984.

The Right Fork of Holly is 23.9 miles long. It begins one mile northeast of the Back Fork of Elk River near Webster Springs and near the long-gone logging town of Skelt, at an elevation of 3,450 feet. It drops to an elevation of 950 feet at the junction of the two forks.

Main Holly River is the shortest river in West Virginia. It is only slightly more than three miles from where the two forks meet to the river's entrance into Sutton Lake at Holly Point, the bluff that overlooks the lake at the mouth of Holly. Formerly the Holly entered Elk River at this place.

The Palmer Lumber Company built a large band mill at the mouth of Holly in the 1890s and brought logs there from its extensive timber holdings in the Holly watershed. The company extended the West Virginia & Pittsburg [sic] Railroad from Holly Junction, just below the mouth of the river, to the sawmill, and from there up main Holly and the LeftFork. Later, John T. McGraw, a railroad tycoon at the start of the 20th century, bought the Palmer holdings, renamed the railroad the West Virginia Midland, and extended it up the Right Fork, where it meandered over Elk Mountain to Webster Springs.

Holly River State Park is located on the headwaters of the Left Fork of Holly River.