Prior to completion of the Lyons Ferry Fish Hatchery, a portion of the Snake River stock fall chinook salmon adults were collected and reared at the Kalama Falls Fish Hatchery on the lower Columbia River as part of the Snake River Fall Chinook Egg Bank Program. When the Lyons Ferry facility was completed, eyed eggs were transported from the Kalama Falls Fish Hatchery to Lyons Ferry for rearing and subsequent release. Ocean commercial and recreational fisheries from Alaska to Washington, in addition to Columbia River treaty, non-treaty and sport fisheries all harvest a portion of the Snake River fall chinook. Sport fisheries for spring chinook in the subbasin have been closed since 1978. Average spring discharge has ranged from 1 to 10 kcfs over the last 40 years.
Habitat quality remains high in wilderness areas of the north fork mainstem and Granite Creek.
Screens are currently maintained on several hundred water diversions. Significant habitat improvement efforts began on federal lands in 1973 and on private lands in 1984. Estimated recruits to the Columbia River mouth from these brood years ranged from 1,236 to 6,620. The MFSR has been closed to sport harvest of chinook since 1978. Most of the drainage, including the mainstem, is within the Frank Church River of No Return Wilderness Area.