The South Branch Kishwaukee River originates near Shabbona in DeKalb County and flows approximately 64 miles northeast before turning westward near Genoa, ultimately joining the main Kishwaukee River southeast of Rockford in Winnebago County. This tributary drains 441 square miles and represents the largest branch of the Kishwaukee system by watershed area.

The river's character changes distinctly along its course. Upstream sections near DeKalb feature a channelized, shallow waterway with silty sand substrate and minimal natural vegetation along banks. Below DeKalb, the river transforms into a more natural stream with sandy-gravel bottom, pool-riffle sequences, and vegetated buffers typically exceeding 100 feet. The average width measures 55 feet, though the river receives significant treated wastewater discharge from DeKalb, creating unusual flow patterns where effluent can equal or exceed natural baseflow during low-water periods.

The South Branch flows over moraines deposited during glaciation, with portions of its bed following ancient lake plains. North of Sycamore, gravel mining operations have historically worked the river's rock-strewn substrate. The stream maintains relatively low natural flow rates compared to other Kishwaukee tributaries, with average discharge around 305 cubic feet per second near Fairdale.

Anglers target smallmouth bass in the less-channelized reaches downstream of DeKalb, where improved habitat supports diverse fish populations. The river corridor provides habitat for white-tailed deer, muskrats, herons, and various mussel species in suitable gravel substrate areas. Riparian forests of silver maple, sycamore, and willow dominate the lower reaches.

Access points exist near Kirkland and throughout DeKalb County Forest Preserves, including the Kishwaukee River State Fish and Wildlife Area west of Kirkland, which protects over 900 acres with 3.2 miles of river frontage adjacent to MacQueen and Potawatomi Woods Forest Preserves.

Flood stage at DeKalb begins at 10 feet, with the river historically exceeding this level nine times since 1926. The record crest of 15.8 feet occurred in July 1983, with the second-highest flood reaching 15.27 feet in August 2007 following intense rainfall that displaced 600 residents and closed Northern Illinois University. Paddlers should exercise caution during high-water periods and be aware that upstream channelized sections offer limited scenic or technical interest compared to the more natural downstream reaches approaching the confluence with the main Kishwaukee.