The river begins in a woods 2 kilometres (1.2 mi) southeast of the community of Boothville in the township of Southgate.

The river heads west, over Holstein Dam at the community of Holstein, and under Ontario Highway 6 south of the community of Orchardville.

The Beatty Saugeen turns northwest, passing to the south of the community of Hampden in the township of West Grey, before reaching its mouth at the South Saugeen River on the south side of the town of Hanover.

There are four monitoring stations in the Beatty Saugeen drainage basin: two for Benthic zone animals, one for surface water quality, and one combined.

There are two rare species: the Delta-spotted spiketail and the Hart's Tongue Fern.