Between the North and South forks there is a portion of the Mount Baker-Snoqualmie National Forest called the Boulder River Wilderness.

Collecting many tributary creeks, the river flows south, then west through the foothills along the Skagit-Snohomish county line.

The South Fork (30 miles (48 km)) originates from the northern slopes of Del Campo Peak and Morning Star Peak in central Snohomish County, 20 miles (32 km) south of Darrington, and flows west and northwest by Silverton, Verlot, and Granite Falls.

[4] Hatt Slough flows southwest and is now the primary distributary of the Stillaguamish waters into Port Susan, having been diverted in the early twentieth century.

The river level rises and falls very quickly, with the average north fork flood duration of eight hours.

[3][8][9] Other Indigenous peoples historically traveled to the Stillaguamish River to fish as well, including the Sauk, the Snohomish, and the Duwamish.