[1] Clear Creek is neatly divided by the bluffs of the Mississippi into two sections: nearer its headwaters it is a relatively clean and swift-flowing hill river, and in its lower half, below the bluff, it has become a channelized ditch, the Clear Creek Ditch (coordinates: 37°23′30″N 89°21′11″W / 37.391716°N 89.353143°W / 37.391716; -89.353143).
[2] Clear Creek rises in the uplands of the Shawnee Hills near Cobden, Illinois.
[3] West of Jonesboro, Illinois, Clear Creek descends from the Shawnee Hills into the bottomland of the Mississippi River.
In historical times, the stream fed a ribbon-shaped wetland that ran southward and parallel to the Mississippi River for approximately 15 miles (24 km) before discharging into a former watercourse of the main river, the Picayune Chute, east of Cape Girardeau, Missouri.
Part of this wetland has been conserved as the Union County State Fish and Wildlife Area, but during the 20th century most of it was extensively ditched and drained for mosquito abatement and to promote agriculture.