The value of using environmental tracer profiles in aquitards to quantify fluid flux and to reveal information about palaeohydrology is largely unknown for parts of the world that were not glaciated during the Cenozoic. We present deep, continuous vertical profiles of aquitard pore water chloride concentration and δ2H/δ18O composition from the western margin of the Great Artesian Basin, Australia, where upward leakage is the dominant groundwater discharge mechanism. At the deeper of the two sites studied, the Cl− and δ2H profiles exhibit a distinctive S-shape, which we interpret as a shift in the upper concentration boundary condition over time. Numerical simulations are used to support an hypothesis that the shallow phreatic aquifer was more saline and more enriched in δ2H compared to current conditions prior to ∼120 ka, followed by an extended freshening phase from ∼120 to 20 ka, then a saline phase similar to current conditions for the last ∼20 ka. These timeframes correspond favorably with results of previous studies into the palaeohydrology of nearby playa Lake Eyre. At the shallower site, the tracer profiles decrease exponentially with depth. We explore several models for the evolution of these profiles and adopt one of long-term salt input at ground surface. At both sites, tracer concentrations for groundwater sampled from the underlying artesian aquifer provide conclusive evidence that recharge occurred within the last 10–20 ka. Chloride was a more useful tracer than δ2H in this study, primarily due to lack of recent glaciation in central Australia to provide a dynamic δ2H tracer signal.