To better understand the response of tropical wetlands to Holocene environmental changes, two lacustrine diatom records from Weipa, Cape York, have been investigated. The record from Big Willum (BW01) commenced approx. 7.9 calibrated thousand years before present (k cal a BP) and details stages of initial swamp development, a phase of ephemeral conditions between approximately 5.7 and 2.2 k cal a BP and relative wetland stability after 2.2 k cal a BP. Lithological and to a lesser extent diatom assemblage changes in BW01 appear to be linked to broad-scale changes in effective precipitation. The record from Little Willum (LW01) commenced around 0.9 k cal a BP and documents initial phases of swamp development until approximately 0.8 k cal a BP with subsequent relative wetland stability. The uppermost 10 cm of this record, approximately spanning the last 40 years, coincide with mining activity in the region. Only minor changes in the diatom assemblage are recorded for this period implying that the overall character of the swamp probably remained unchanged. Both sites offer new insights into wetland dynamics in Australia's dry tropics and demonstrate that changes in these lacustrine systems were probably driven by shifts in effective precipitation, in particular during the late Holocene.