Muskegon River is a river in the western portion of the lower peninsula of the U.S. state of Michigan. The river has its headwaters in Houghton Lake in Roscommon County, flowing out of the North Bay into neighboring Missaukee County. From there it flows mostly southwest to Muskegon, Michigan, where it empties into Muskegon Lake. Muskegon Lake is connected to Lake Michigan via a mile-long channel.