It rises in the mountains of central Clatsop County south of Saddle Mountain State Natural Area. It flows WNW then north, parallel to the coast and approximately 5 mi (8 km) inland. It enters the Youngs Bay on the Columbia at Astoria. The site of Fort Clatsop is located approximately 1.5 mi (2.5 km) upstream from the mouth of the river.
The river is widely known in the region as an excellent place to catch the bottom-feeding sturgeon, which is a popular sport fish in the area, and is home to an extensive salmon repopulation program, just outside of Astoria, Oregon proper, that is currently run by the Oregon Department of Fish and Wildlife. The salmon fry, called "fingerlings" can be seen writhing and jumping within their net-lined pens along the river's eastern banks.