The river begins at an elevation of 395 metres (1,296 ft) at Cunning Bay on Wollaston Lake.

It flows north to Hatchet Lake at an elevation of 393 metres (1,289 ft) and continues to Waterfound Bay at an elevation of 376 metres (1,234 ft), where the tributary Waterfound River enters from the left.

The river continues north to Kosdaw Lake at an elevation of 364 metres (1,194 ft), over the Redbank Falls to Otter Lake, the Manitou Falls, the Brink Rapids and the Brassy Rapids, before the Hawkrock River enters from the left.

The Fond du Lac River flows further over the Perch Rapids, takes in the Porcupine River from the right, travels over the Burr Falls, and enters Black Lake at an elevation of 276 metres (906 ft).

These include walleye, yellow perch, northern pike, lake trout, Arctic grayling, lake whitefish, cisco, white sucker, longnose sucker and burbot.