The Partridge River rises in Bertha Township north of the town of Eagle Bend on The Harren Farm in northwestern Todd County and flows generally northeastwardly into southeastern Wadena County, past the town of Aldrich. It joins the Crow Wing River in Thomastown Township, about 9 miles (14 km) north-northwest of the town of Staples and about 1 mile (2 km) downstream of the mouth of the Leaf River.
Its largest tributary is the Little Partridge River, which rises west of Eagle Bend in Wykeham Township in Todd County and flows 21.1 miles (33.9 km) northeastwardly,[2] parallel to the uppermost stretch of the Partridge River, which it joins in Bartlett Township.