The river is 140 mi /225 km long and in the Neosho River Drainage Basin. Cottonwood Rivers two stream branches rise in western Marion County, flowing to the southeast. Joined by smaller creeks as the river grows and turns northeasterly in Chase County. Becoming a tributary to the Neosho River in Lyon County. The region is subject to intense storms, especially during the late spring and early summer and again in autumn. The Neosho River and its principal tributary, the Cottonwood River, occupy wide valleys, large portions of which may be inundated during floods.
Public access to the river includes:
- Emporia - Emporia Peter Pan Park
- Emporia Soden Park
- The town of Cottonwood Falls