The Root River watershed covers over 1600 square miles and is a little larger than either the Cannon River or the Zumbro River, but it seems much larger because the watershed includes more streams, valleys, and hills. Also, more of the Root's watershed is put to recreational use than to agriculture. Almost the entire network of rivers and streams lies in a system of steep coulees, timbered slopes, rushing streams, and deep, winding valleys.

The Root River has three main branches - North, Middle, and South.

The North and Middle branches join south of Chatfield and the South branch comes in near Lanesboro.

The South Fork, which flows through the Yucatan Valley, enters the main stem of the root by Houston.

The Middle Branch has three tributaries, Bear Creek, Deer Creek, and Spring Valley Creek, whose routes also are included in the guide "Canoeing the Driftless".

The name Root is derived from a Sioux name for the stream, and possibly refers to tree roots exposed along the stream after floods. The Sioux word for “root” was hokah or hutkan, and the little town of Hokah on the river reflects this origin. The canoeable routes of the
Root River and its tributaries total more than 240 miles.

The Root River’s great scenery combined with the DNR accesses, available canoe and kayak rental and shuttle service make it suitable for family canoe day trips or for the more adventurous, overnight trips using the designated DNR canoe campsites. The routes of the Root River are described in the guide "Canoeing the Driftless" in two sections:

o The first section contains the routes on the main branch that are suitable for beginners and experienced paddlers, have DNR maintained accesses, and are serviced by several canoe outfitters in Lanesboro, Chatfield, Whalen, Houston and Rushford.

o The second section describes routes of the less traveled, small, narrow branches and forks of the Root River that are suited for experienced paddlers using solo canoes or kayaks.