The entire length of the Pinnebog lies within Huron County and is fed by various agricultural ditches and drains.

It flows southwest for about 2 miles (3 km) around the unincorporated community of Popple where it is fed by the Cameron and McLean drains.

It then bends northward around Popple and flows northwest for about 5 miles (8 km) past the east side of the village of Elkton.

Before reaching Lake Huron, it turns to flow east-northeast for about 3 miles (5 km) to its mouth.

The river's watershed drains all or portions of the following townships: Bingham, Chandler, Colfax, Dwight, Hume, Lake, Lincoln, Meade, Oliver, Sheridan, and Verona.