The flow of the creek depends on monsoonal rains falling months earlier and many hundreds of kilometres away in eastern Queensland.

[5] It rises west of the Great Dividing Range on low ground as two central Queensland rivers, the Thomson between Longreach and Charters Towers, and the Barcoo in the area east of Tambo.

[6] Studies have clearly shown that, although with a mean annual flow of around 2.3 cubic kilometres (0.55 cu mi) (ranging at Barcoo from an estimated 0.02 km3 or 16,000 acre⋅ft in 1902 to an estimated 12 km3 or 2.9 cu mi in 1950) the Cooper carries twice as much runoff as the Diamantina and three times as much as the Georgina, over the past ten thousand years it has reached Lake Eyre much less frequently than those rivers.

This is because much more water is absorbed along its course than with the Diamantina or Georgina, but may also be because of centennial or multicentennial wet and dry cycles in those basins causing them to regularly reach the lake during wet periods (there is some evidence from terraces around Lake Eyre that this occurred during the Medieval Warm Period).

The soils are mainly Vertisols or Vertic Torrifluvents and are quite fertile, though generally heavy in texture with a strong tendency to crack due to the erratic rainfall.