[4] The river, which has a notable higher western bank, begins with three separate branches that flow into the Horicon Marsh.

The South Branch rises north of Fox Lake in Dodge County and flows east through Waupun to the marsh.

[6] In northern Rock County, Wisconsin, it receives the Yahara River, and flows southward through tiny Fulton, Janesville and Beloit into northern Illinois, where it receives the Pecatonica River 5 miles (8 km) south of the state line.

It flows south through Rockford, then southwest across northwestern Illinois, picking up the Kishwaukee River, passing Oregon (here, on a high bluff overlooking the river is the Eternal Indian sculpture), Dixon, Sterling (which has the Sinnissippi Mounds national historic site and local park) and Rock Falls before joining the Mississippi at Rock Island.

[11] The river is also home to the Rock Aqua Jays, an amateur water ski club that performs at Traxler Park in downtown Janesville, Wisconsin.