Late in the season, as the draw-downs decrease with the cooler weather, more water is released into the stream, allowing fish to move up from the lower section of the river.

The river flows south through a high plateau in northern Fremont County, through the Caribou-Targhee National Forest, and passes through Island Park Reservoir.

It emerges from the reservoir and flows through a canyon that opens up into a broad, flat meadow in the Island Park Caldera in central Fremont County.

The river flows slowly past the town of Island Park, through the Harriman State Park, otherwise known as the "Railroad Ranch", and then descends swiftly as it approaches the wall of the caldera, flowing over both Upper Mesa and Lower Mesa Falls, and emerges from the mountains onto the Snake River Plain near Ashton.

It flows southwest across the plain, past St. Anthony, and splits into multiple channels into a broad inland delta north of Rexburg.