The river and its forks rise near in the Alpine Lakes Wilderness area of Mount Baker-Snoqualmie National Forest in the Cascade Mountains and flows generally north, joining the Tye River to form the South Fork Skykomish River.

[2] The East Fork Foss River originates at 47°34′41″N 121°10′53″W / 47.57806°N 121.18139°W / 47.57806; -121.18139,[3] from the meltwater of Lynch Glacier on the north slope of Mount Daniel.

The East Fork Foss River flows generally north, joining the West Fork to form the main stem Foss River.

[2] The West Fork Foss River originates at 47°33′29″N 121°17′24″W / 47.55806°N 121.29000°W / 47.55806; -121.29000,[4] from a small glacier and lake on the north side of Iron Cap Mountain.

Leaving the lakes region the West Fork flows generally north, joining the East Fork to form the main stem Foss River.