It originates in several forks in southwestern Washington, flows east, then north, then west, in a large curve, before emptying into Grays Harbor, an estuary of the Pacific Ocean.

The river's mouth was out near current Westport until rising sea levels at the end of the ice age flooded the broad Chehalis Valley to form a ria, known today as Grays Harbor.

Though the people ceded the lands surrounding the Chehalis River upon the signing of the 1856 Treaty of Olympia, the tribes have retained fishing and hatchery rights.

[9] During the Great Coastal Gale of 2007, a 20-mile (32 km) stretch of Interstate 5 was closed between exits 68 and 88 because of flooding from the Chehalis River, causing the roadway to be under about 10 feet (3.0 m) of water.

Since the main east–west mountain passes were also closed during this event, the flooding from the Chehalis River essentially cut off interstate traffic to the Puget Sound area from the south, and no detour was available.

The waterway is an economic necessity, and a source for food, water, and recreation for several large cities, such as Aberdeen, Centralia, Chehalis, and Hoquiam.

From there the Chehalis flows north and east, collecting tributary streams that drain the Willapa Hills and other low mountains of southwestern Washington.

Known as the Chehalis Basin Flood Warning System, it expanded a sensor network already in place, providing information on rainfall and temperature, as well as additional gauges.

[25][26] The river is home to several salmon species, including chum, coho and Fall Chinook, and the basin is also a habitat for Steelhead trout.