The headwaters of the Lort River begin in the Peak Charles National Park and its surrounding vacant Crown land. The river flows in a south-westerly direction and enters farmland area for a distance of 45 kilometres (28 mi) with a reserve that is an average of 500 metres (1,640 ft) wide containing riparian vegetation. The river then enters the Stokes National Park before discharging into Stokes Inlet.
The catchment of the river has been extensively cleared for Agricultural purposes. It is estimated that 60% of the catchment has been cleared; this has led to increased sedimentation, eutrophication and salinity levels of the river.