The headwaters of the Prophet River can be found in the Bruce Ridge of the Muskwa Ranges in the Northern Rockies, at an elevation of . It flows eastwards between the Northern Rocky Mountains Provincial Park and the Redfern-Keily Provincial Park, with occasional waterfalls on its course. The remote Prophet River Hotsprings Provincial Park is established on the upper course of the river. It receives the waters from Hewer Creek north of Mount Boe, then from Kravac Creek and Richards Creek towards the foothills. North of Klingzut Mountain it receives the Besa River just before flowing from the mountains into the plains