Abstract Climates of the last two millennia have been the focus of numerous studies due to the availability of high-resolution palaeoclimate records and the occurrence of divergent periods of climate, commonly referred to as the ‘Medieval Climatic Anomaly’ and ‘The Little Ice Age’. The majority of these studies are centred in the Northern Hemisphere and, in comparison, the Southern Hemisphere is relatively under-studied. In Australia, there are few high-resolution, palaeoclimate studies spanning a millennium or more and, consequently, knowledge of long-term natural climate variability is limited for much of the continent. South-eastern Australia, which recently experienced a severe, decade-long drought, is one such region. Results are presented of investigations from two crater lakes in the south-east of mainland Australia. Fluctuations in lake-water conductivity, a proxy for effective moisture, are reconstructed at sub-decadal resolution over the past 1500 years using a statistically robust, diatom-conductivity transfer function. These data are interpreted in conjunction with diatom autecology. The records display coherent patterns of change at centennial scale, signifying that both lakes responded to regional-scale climate forcing, though the nature of that response varied between sites due to differing lake morphometry. Both sites provide evidence for a multi-decadal drought, commencing ca 650 AD, and a period of variable climate between ca 850 and 1400 AD. From ca 1400–1880 AD, coincident with the timing of the ‘Little Ice Age’, climates of the region are characterised by high effective moisture and a marked reduction in inter-decadal variability. The records provide context for climates of the historical period and reveal the potential for more extreme droughts and more variable climate than that experienced since European settlement of the region ca 170 years ago.