Optically stimulated and thermoluminescence ages from relict shorelines, along with accelerator mass spectrometer 14C ages from freshwater molluscs reveal a record of variable moisture sources supplied by northern and southern river systems to Lake Mega-Frome in southern central Australia during the late Quaternary. Additional lacustrine, palynological and terrestrial proxies are used to reconstruct a record that extends back to 105 ka, confirming that Lakes Mega-Frome and Mega-Eyre were joined to create the largest system of palaeolakes on the Australian continent as recently as 50–47 ka. The palaeohydrological record indicates a progressive shift to more arid conditions, with marked drying after 45 ka. Subsequently, Lake Mega-Frome has filled independently at 33–31 ka and at the termination of the Last Glacial Maximum to volumes some 40 times those of today. Further sequentially declining filling episodes (to volumes 25–10 those of today) occurred immediately prior to the Younger Dryas stadial, in the mid Holocene and during the medieval climatic anomaly. Southern hemisphere summer insolation maxima are a poor predictor of palaeolake-filling episodes. An examination of multiple active moisture sources suggests that palaeolake phases were driven independently of insolation and at times by some combination of enhanced Southern Ocean circulation and strengthened tropical moisture sources.