The semi-arid Australian continental inland is increasingly subject to climatic extremes such as drought and flooding. Combined with the exceptionally low topographic relief characteristic of this region, hydroclimatic extremes can have an enormous impact on the land surface. Nevertheless our understanding of dryland hydrologic connectivity and earth-surface response remains poorly understood and largely unquantified. Here we investigate the impact of past hydroclimate on the semi-arid Willandra Lakes over the last 60 ky, integrating sediment-based chronologies for filling and drying of multiple basins with water-flux modelling and reconstruction of palaeoclimate parameters. We quantify the threshold inflow volume required to fill the lake system to 2 km3. We establish that prior to 25 ka, permanent lakes persisted for protracted periods of time in response to increased catchment precipitation, consistent with regional geomorphic indicators for wetter conditions. By contrast, the Last Glacial Maximum (LGM) oversaw rapid couplets of lake filling and drying despite lower precipitation, temperature, and increasing evaporation. We propose that seasonal snow melt from the highland headwaters during this cold phase, coupled with increased effective runoff due to reduced vegetation cover, was responsible for the large quantities of water entering the system at this time.