The BNSF Railway's line through Flathead Tunnel and Marias Pass follows part of the lower Fisher River and its tributary Wolf Creek.

Much of the land of the Fisher River basin is privately owned, but a large portion lies within Kootenai National Forest.

[6] In the late 1960s, the Great Northern Railway (BNSF today) was rerouted along the lower ten miles (16 km) of Fisher River and most of Wolf Creek, a tributary.

Portions of Pleasant Valley Fisher River have also been channelized and shortened along U.S. Highway 2.

All of these things negatively impact fish habitat in the Fisher River basin.