The identification of wetter and drier phases from the last deglaciation to the Late Holocene has been a valuable outcome of palaeoenvironmental (chiefly palynological) studies of northeastern Australia conducted over the past 40 years. Few studies have, however, focussed on the identification of wetter and drier phases in the wet tropics, and none have set their focus on the last 4000 years, a period when northeastern Australia is generally accepted to have experienced increased El Niño/Southern Oscillation (ENSO) activity. The present study provides this palaeoclimatic information using the degree of peat humification as the main palaeoclimatic proxy. To identify regional climatic signals in the peat record and differentiate these from local signals induced by particular basin hydrology or ecology, sedimentary sequences from two geographically separated swamps on the Atherton Tableland in north Queensland are examined. Wet and dry shifts are detected in the humification records for Bromfield Swamp (core BSAT03) and Mount Quincan crater swamp (Q2). Seventeen wet shifts are detected in both records with 12 shifts showing good cross-correlation at the following dates (with 2σ range): 3990/3960 (4090–3850), 3480/3550 (3640–3420), 2950/2990 (3080–2790), 2860/2880 (2980–2700), 2560/2610 (2730–2450), 1880/1820 (2100–1740), 1430/1410 (1660–1320), 1170/1080 (1390–1020), 990/1010 (1100–790), 610/640 (710–490), 290/300 (330–180) and 120/150 (190–40) cal. yr BP. A particular dry phase, initiated by dry shifts at 4090 cal. yr BP (Bromfield Swamp) and 4330 cal. yr BP (Mount Quincan), reaches its greatest strength at 4050 cal. yr BP.