Sum probability analysis of 1275 radiometric ages from 608 archaeological sites across northern and central Australia demonstrates a changing archaeological signature that can be closely correlated with climate variability over the last 2 ka. Results reveal a marked increase in archaeological records across northern and central Australia over the last 2 ka, with notable declines in western and northern Australia between ca. AD 700 and 1000 and post-AD 1500 – two periods broadly coeval with the Medieval Climatic Anomaly and the Little Ice Age as they have been documented in the Asia–Pacific region. Latitudinal and longitudinal analysis of the dataset suggests the increase in archaeological footprint was continent wide, while the declines were greatest from 9 to 20° S, 110 to 135° E and 143 to 150° E. The change in the archaeological data suggests that, combined with an increase in population over the late Holocene, a disruption or reorganisation of pre-European resource systems occurred across Australia between ca. AD 700 and 1000 and post-AD 1500. These archaeological responses can be broadly correlated with transitions of the El Niño–Southern Oscillation (ENSO) mean state on a multi-decadal to centennial timescale. The latter involve a shift towards the La Niña-like mean state with wetter conditions in the Australian region between AD 700 and 1150. A transition period in ENSO mean state occurred across Australia during AD 1150–1300, with persistent El Niño-like and drier conditions to ca. AD 1500, and increasing ENSO variability post-AD 1500 to the present.