With 500 miles of undammed waters, the John Day River is the second-longest free-flowing river in the continental United States. Much of the Lower John Day flows through proposed wilderness areas, while the upper river provides critical habitat for the largest and most diverse native fish populations in Oregon. Among the species that call this river home are endangered bull trout and summer steelhead, along with chinook salmon, redband trout, and westslope cutthroat trout.

The John Day also provides Oregonians with unparalleled recreational opportunities. On the river's mainstem, boating is the most popular activity, with flyfishing coming in a close second. All of these outstanding qualities – wild fish, recreation, and potential wilderness – led Congress to designate 200 miles of the John Day as a wild and scenic river in 1988.

Streamside grazing along the John Day contributed to ecological damage, including water pollution, soil compaction, bank erosion, and increased water temperatures due to reduction in streamside shading.  ONDA is working to remove grazing from along the John Day River and tributaries through permit retirement and enforcing protection mandated by its Wild and Scenic status.