The John Day River remains the longest undammed tributary of the mighty Columbia River. With only two dams below the confluence with the Columbia and hundreds of river miles of spawning habitat scattered among its many tributaries, the John Day River serves as a vital spawning ground for the spring chinook salmon and summer steelhead that have fought their way upstream.
Adult chinook usually pass through the John Day Fossil Beds on their upstream trek from April to June, while adult steelhead may head up anywhere between August and May depending on the river flows. Some rearing of young steelhead occurs within the monument, but this section of the river primarily serves as a conduit for the smolts of both species to head out to the Pacific Ocean. In recent times, the importance of the John Day Basin in the life cycle of Pacific lamprey eels has also been noted in research.
Bridgelip suckers, northern pikeminnow, redside shiners, and chiselmouth chub along with introduced smallmouth bass are able to better tolerate warmer summer river temperatures. From October through June, cooler water species such as the salmon and steelhead fry, redband trout, and Paiute sculpin can be found as they move down from the upper watershed.
The monument has made a concerted effort to remove or replace the irrigation water diversions found in the John Day River or Rock Creek that were once barriers to fish movements. Restoration of the cottonwood galleries and other trees that historically provided shade relief from the hot summer sun is ongoing. These trees will also provide leaf matter for the many aquatic insects so important to the aquatic food chain.
State fishing regulations apply, except that fishing for bullfrogs and crayfish is prohibited within John Day Fossil Beds National Monument.