Riparian (streamside) vegetation along the Middle Fork John Day River has been drastically reduced from historic levels, by as much as 100% in some reaches. In general, areas with wide floodplains have been most affected because these areas were historically used for agriculture or mining. Loss of riparian cover decreases shade, which raises water temperature, sometimes to lethally warm levels for salmon and steelhead. Loss of vegetation also reduces channel stability due lack of root structures to protect the banks form erosion. Without riparian forest cover there is also no source of large woody debris to streams, which provides fish with places to hide, rest and feed. Streamside vegetation also provides nutrients and leaf litter to the stream, which are important for fueling stream insects and fish.

Some types of riparian fencing and planting projects include replanting native woody vegetation such as willow and alder; creating cattle exclosures around riparian areas; and fencing aspen stands.