Together with the north and south branches, the river system has approximately 22 miles (35 km) of mainstream and the water basin drains 40,320 acres (163.2 km2).

[3] The North Branch Boyne River is 5.9 miles (9.5 km) long[1] and rises in Hudson Township in eastern Charlevoix County at 45°10′34″N 84°48′52″W / 45.17611°N 84.81444°W / 45.17611; -84.81444.

[4] The South Branch Boyne River is 10.5 miles (16.9 km) long[1] and rises in Elmira Township in northwest Otsego County at 45°05′10″N 84°48′42″W / 45.08611°N 84.81167°W / 45.08611; -84.81167.

[5] The South Branch flows northwest across the northeast corner of Warner Township in Antrim County.

The river system has three major impoundments: The soils surrounding Boyne River's headwaters are primarily composed of a Kalkaska-Leelanau association (a mixture of Kalkaska and Leelanau sands), and tend to form steep riverbanks.