The Baraboo River rises in southeastern Monroe County and flows generally southeastwardly through Juneau, Sauk and Columbia Counties, past Kendall, Elroy, Union Center, Wonewoc, La Valle, Reedsburg, Rock Springs, North Freedom, West Baraboo and Baraboo.
In its upper course above Elroy, the river is paralleled by the Elroy-Sparta Bike Trail.