The Burdekin River rises on the western slopes of the Seaview Range, part of the Great Dividing Range, west of . In the river's upper catchment, from its source the river generally flows west and then south out of the Girringun National Park, part of the UNESCO Wet Tropics World Heritage Area. This area, now part of Basalt was the location of one of the earliest inland settlements in northern Australia and was known as Dalrymple. The river is joined by Lucy Creek, the Running River, Star River and Keelbottom Creek, above . From the west in the Dry Tropics to the west of the river, the river is joined by the Clarke, Basalt and Dry rivers. South of Charters Towers, the upper catchment of the Burdekin River is joined by the Fanning River, and then continues to flow south through wetlands before entering Lake Dalrymple, the reservoir created by the Burdekin Dam.