Streams may receive water from different sources in their catchments. There is limited understanding of which water stores intermittent streams are connected to. Using geochemical/environmental tracers, we show that the intermittent streams in southeast Australia are connected to younger smaller near-river water stores rather than regional groundwater and groundwater inflows to the streams are relatively limited. This makes these streams more vulnerable to the impacts of climate change and requires management of the riparian zone for their protection and the effects of potentially contaminated groundwater on streams and their ecosystems will also be lessened.