At Kimberly in northwestern Grant County, it is joined from the east by the North Fork John Day River (which had already joined with the Middle Fork John Day River above Monument, Grant County, Oregon). The river then flows west across Wheeler County. At the county line with Jefferson County it flows north, past the Clarno Unit of the John Day Fossil Beds National Monument. As it approaches the Columbia River in north-central Oregon it flows in an increasingly meandering course, forming the boundary between Sherman County to the west and Gilliam County to the east.