The Boardman River watershed is in Grand Traverse and Kalkaska counties and includes 180 miles of river and tributary streams. The watershed covers 287 square miles and drains 182,800 acres of land. The Boardman River is a subwatershed of the Grand Traverse Bay watershed, making up almost a third of the land area and tributary inputs of water into Grand Traverse Bay. As such, the Boardman River watershed plays a large role in the ecological health of Grand Traverse Bay.

The Boardman River is one of the top ten trout streams in Michigan, with 36 river miles designated as a Blue Ribbon trout stream. Sections of the river are a state-designated Natural River, which afford specific protection for preservation in a natural condition. Historically, the Boardman River was an Arctic grayling fishery, with brook trout, brown trout, and rainbow trout introduced in the 19th and 20th centuries. The river now has self-sustaining populations of brown, brook, and resident rainbow trout as well as migratory rainbow trout and Chinook and coho salmon. The river flows into and through Boardman Lake, which supports typical warm-water game fish populations.

The river is a primary contributor to the quality of life for the surrounding cities and townships. It is a major recreational draw for both residents and visitors, with estimates of as many as two million user days logged on the river annually for recreation purposes. Many of these visitors come to paddle, fish, and hike.

Historically, five dams were located on the Boardman River (Union Street, Sabin, Boardman, Keystone, and Brown Bridge). Currently, only Union Street dam is still in place; Keystone dam washed out in 1961, Brown Bridge dam was removed in 2012, Boardman Dam was removed in 2017, and Sabin Dam was removed in 2018. The recent Boardman River Dams Ecosystem and Restoration Project reconnected over 160 miles of free-flowing, cold-water stream and restored hundreds of acres of wetland and upland habitat.