The Lower Baraboo River lies in eastern Sauk County and western Columbia County. It includes the Baraboo River and its tributaries downstream of Baraboo and streams draining to the Wisconsin River in Sauk and Columbia counties from below Wisconsin Dells to the Columbia electric power generating plant. Pine Island State Wildlife Area is in the watershed. There are two major municipal wastewater dischargers in the watershed, Baraboo and Portage.
Agriculture is predominant, with dairying and large muck farms the primary activity.
The north slope of the Baraboo Range, a Precambrian inlier set of hills, is in the watershed. These hills are heavily wooded and have unique sub-ecosystems containing rare plant species. The cities of Baraboo and Portage are in this watershed. The lake is a popular recreation area and has a diverse sport fishery. The lake has been nominated for addition to the state's antidegradation list as an outstanding resource water.