The headwaters of the Rudall and Cotton Rivers are in the northern limits of the bioregion in Western Australia. The Rudall River is a significant wetland/ecological refuge, which contains major permanent waterholes and soaks. The Rudall River flows approximately 120km into Lake Dora (30, 000ha) in the Western Australian sector of the bioregion.
In the northwest of the bioregion is Dragon Tree Soak, a 5ha swamp regarded as a relict of the riverine vegetation found along the palaeo-river in the wetter climates of the early to mid Holocene. The soak is a fresh water spring that supplies freshwater to the marsh and peatland.
Lake Amadeus is a massive saline lake in the Northern Territory, which has no significant surface inflow. The main inflow of water is via groundwater seepage.