[5] The Shell River issues from Shell Lake approximately 3 miles (5 km) southwest of Pine Point in Carsonville Township in eastern Becker County, and initially flows southeastwardly through the Smoky Hills State Forest into southwestern Hubbard County and northwestern Wadena County, to Blueberry Lake, which collects the Blueberry River.

From Blueberry Lake, the Shell River flows eastwardly in a winding course through northern Wadena and southern Hubbard counties, passing through Huntersville State Forest and collecting the Fish Hook River from the north.

[6] The Shell River is the Crow Wing River's first significant tributary, and is substantially the larger of the two at their confluence; the Shell's average discharge of 250 cubic feet per second (7 m³/s) is approximately three times the Crow Wing's discharge above the confluence.

[4] The Shell River flows in the Northern Lakes and Forests ecoregion, which is characterized by conifer and hardwood forests on flat and rolling till plains and outwash plains.

[7] The lower course of the river below Blueberry Lake can be canoed, and supports a sport fishing population of northern pike.