In southeast Lafayette County it receives the East Branch Pecatonica River, approximately 8 miles (13 km) north of the state line.

It flows south-southeast into Illinois, past Freeport, where it turns east, then east-northeast, receiving the Sugar River near Shirland in northern Winnebago County, 5 miles (8 km) south of the state line.

The 142-acre (57 ha) Pecatonica Woodlands Preserve contains bottomland forest, oxbow pond, wetland, and sedge meadow habitats.

The Pecatonica River Woods SNA was listed on the basis of possessing a diverse range of forest ecosystems, from southern dry, through mesic, to floodplain.

The 52-acre (21 ha) Weir White Oaks State Natural Area, a privately owned preserve managed by the Wisconsin DNR, contains high-quality old growth upland forest and was designated a state natural area in 2002.