The Blackfoot River's drainage basin is approximately 1,097 square miles (2,841 km2) in area.

[4] Its mean annual discharge, as measured at by USGS gage 13068501 (Combination Blackfoot River and Bypass Channel near Blackfoot, Idaho), is 210 cubic feet per second (5.95 m3/s), with a maximum daily recorded flow of 2,130 cu ft/s (60.3 m3/s), and a minimum of zero flow.

The Blackfoot River is formed by the joining of Diamond and Lanes creeks, in the Caribou-Targhee National Forest in Caribou County near Soda Springs, Idaho.

It flows northwest through the Blackfoot Reservoir, which is used for irrigation and flood control, then west to join the Snake River in Bingham County.

The Blackfoot Narrows traverses a desert canyon of primarily sagebrush and juniper habitat: an excellent place to view birds of prey.