The river begins in the Osprey Wetland Conservation Lands and flows generally north-west about 160 kilometres (99 mi) before exiting into Lake Huron.

Another source is more specific, indicating that "Saugeen" is the corrupted form of the Ojibwa word meaning the entrance or mouth of the river.

After leaving Wareham, the river turns west again before then flowing southwest and crossing Ontario Highway 10.

The Saugeen River then continues flowing west until it makes a sharp north turn near the town of Walkerton.

The Saugeen then turns west and enters the town of Southampton; it crosses Ontario Highway 21 at the Zgaa-biig-ni-gan Bridge before emptying into Lake Huron.

This can be done over a three-day trip, including three short portages around dams, and takes in conditions from placid sections to modest rapids and eddies.

In fact, the only known population of Hungerford's crawling water beetles outside of the United States were discovered near Scone in Bruce County, Ontario.