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Temperate Highland Peat Swamps on Sandstone (THPSS) in Eastern Australia are Groundwater Dependent Terrestrial Ecosystems that occur in the headwaters of streams on low relief plateaus. Like upland swamps and peatlands globally, they provide base flow to downstream catchments. However, these swamps are subject to aquifer interference from mining and groundwater extraction and are threatened by urbanization and climate change. We collected winter and summer water samples from swamps in two highland regions of Eastern Australia. Water from the swamps was analyzed for hydrogen (H-2) and oxygen (O-18) isotopes and compared with rainwater, surface water and groundwater samples from the surrounding bedrock aquifers to identify likely swamp water sources. Radon (Rn-222) was used as an environmental tracer to determine whether the swamps were predominantly groundwater or rainwater fed. Four out of five swamps sampled in the Blue Mountains had greater than 30% of water derived from the surrounding bedrock aquifer, whereas swamps in the Southern Highlands received less than 15% of water from the surrounding aquifer. The water sources for swamps in both regions are controlled by catchment morphology, e.g., valley shape. Understanding water sources of these systems is critical for the determination of likely impacts on THPSS from aquifer interference activities and a changing climate.