It drains a timber-producing area in the foothills of the Northern Oregon Coast Range north-northwest of Portland.

It rises in eastern Columbia County, approximately 10 miles (16 km) west of St. Helens on the northern slopes of Bunker Hill.

Major tributaries include Carcus Creek and the North Fork of the Clatskanie, which converge at Swedetown.

It flows generally north-northwest through the Clatsop State Forest, past Clatskanie.

The Clatskanie River converges with Conyers Creek and Beaver Creek near Clatskanie and then it enters a slough on the Columbia from the south approximately 5 miles (8 km) east of Westport.