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.