The Clowhom originates at the outlet of a tiny, unnamed lake on the south slopes of Mount Jimmy Jimmy. It flows south from there for about 4.4 km until it enters remote Phantom Lake. The river turns east upon exiting Phantom Lake and very soon drops over tall Phantom Falls, which is rumored to stand at least 500 feet high. From Phantom Falls, the river runs east for about 4.4 km before turning south for about 5.7 miles and then southwest for about 5 km before entering the north end of Clowhom Lake. The river flows through a dam upon exiting the south end of Clowhom Lake. It only flows about 0.3 km from the lake outlet as it soon reaches its mouth in the Salmon Inlet.