Most of the Deschutes River is designated as a Federal Wild and Scenic River and State Scenic Waterway; and the wide range of habitats in this watershed support a diversity of plants, fish and wildlife.

The Deschutes River and its tributaries historically supported a wide variety of native resident and anadromous fish. Summer steelhead, spring chinook, fall Chinook, bull trout, redband trout, Pacific lamprey and sockeye salmon are among the fish that historically spawned in the Deschutes Basin. Habitat degradation caused by water resource development and by land use changes have extirpated these fish from many streams and limited the populations of those that still exist. Currently, rivers and streams in the Deschutes Basin still support spring Chinook, kokanee, bull trout, redband trout, and Pacific Lamprey, among other species.

Healthy fish populations require healthy upland and riparian zones. Upstream reaches of the Deschutes River and its tributaries pass through forests filled with fir, Douglas-fir, and hemlock. As the elevation decreases, lodgepole pines, ponderosa pines, and meadows begin to replace firs and hemlocks. Further downstream, sage and juniper begin to dominate the landscape. Alders, willows, cottonwoods, and dogwoods provide riparian cover that supports both fish and wildlife. Downstream from Bend, the drier climate supports upland sage and juniper communities. Willows, sedges, and juniper provide riparian cover along the lower Deschutes River and its tributaries (Deschutes Subbasin Plan 2004).