Waterloo Creek is a 9.7-mile-long (15.6 km) tributary of the Upper Iowa River, with a watershed covering 48.3 square miles (125 km2). It rises as Bee Creek in Houston County, Minnesota, southwest of the city of Spring Grove, flowing generally in a southeasterly direction, crossing into Waterloo Township in Allamakee County, Iowa, where it becomes Waterloo Creek and takes a generally north-south route to its confluence with Bear Creek, just before entering the Upper Iowa River. Iowa Highway 76 parallels the stream until crossing the river. The town of Dorchester, Iowa is the only settlement alongside it.