The river flows through the city of Amery and the villages of Star Prairie and Somerset.

It joins the St. Croix River 7 miles (11 km) northeast of Stillwater, Minnesota.

The Apple River was once an important route of trade for the logging industry; timber was floated downstream from logging camps in the north to a sawmill in Amery, Wisconsin where it was cut, loaded onto trains and transported throughout the region.

Today, the river generates tourism revenue through recreation and resorts, attracting 500,000 visitors a year.

On July 30, 2022, Nicolae Miu, a then-52-year-old Romanian-American man,[2] stabbed and killed 17-year-old Isaac Schuman and injured four other people near the sunrise bridge in the town of Somerset.