Part of the Fitzroy River system, the Dee River rises in the Razorback Range south of Bouldercombe Gorge Resources Reserve near Mount Gavial, south of Bouldercombe.

The river flows generally south by west through the mining settlement of Mount Morgan, Waluml and Dululu, where the river is crossed by the Burnett Highway.

The largest dam on the river is Number 7 Dam, built for the Mount Morgan Mine, which has a history of acid mine discharge from gold and copper mining entering the Dee River.

[3] Approximately 700 millimetres (28 in) of rain fell after ex-tropical Cyclone Oswald resulted in the 2013 Eastern Australia floods.

Towards the end of February the dam was spilling acid and heavy metals into the river.