The Dee River rises in the Razorback Range south of Bouldercombe Gorge Resources Reserve near Bouldercombe. Tributaries include Limestone Creek, Horse Creek, Hamilton Creek and Nine Mile Creek on the left while Boulder Creek, Oaky Creek and Pruce Creek enter from the right. The Dee River joins the Don River near Rannes.
In January 2013, the mine pit overflowed for the first time ever. 700 mm of rain fell after ex-tropical Cyclone Oswald resulted in the 2013 Eastern Australia floods. Towards the end of February the dam was still spilling acid and heavy metals into the river. Concerns regarding the discolouration of the river's water and fears of contamination causing irreversible damage to the river were raised in mid-2011.