Palynological records from Holocene wetland deposits in East Polynesia have demonstrated widespread ecological changes following Polynesian arrival after c. ad 1200, but linking inferences of human activities to archaeological records has been limited by equivocal fossil proxies and a lack of chronological controls. To address these limitations, multiple sedimentary profiles were examined from a coastal marsh on the remote East Polynesian island of Rapa. These profiles span 8000 years of ecological change and record mid-Holocene sea-level highstand conditions which receded to modern levels by ad 500. Depositional models were constructed for each profile using Bayesian inferences to characterise the spatial and temporal changes in fossil proxy representation. Just prior to human arrival there are high pollen concentrations of Pandanus and the presence of an extinct palm, both indicative of an extensive lowland swamp forest that developed after ad 500. Indicators of Polynesian arrival and agricultural expansion include unprecedented amounts of charcoal particles and pollen from the introduced cultigen, Colocasia esculenta (taro). The swamp forest was progressively cleared, beginning in the most inland section at ad 1110-1230. The Colocasia-based agricultural system reached its greatest extent from ad 1590 to 1740. The last appearance of the extinct palm was recorded at ad 1520-1660 and the entire area was cleared of indigenous trees soon after European colonisation at ad 1830-1880. By modelling the chronologies of individual fossil proxies across each profile, we have developed a framework for defining the processes behind vegetation change and for matching palynological-based inferences of human activity with archaeological records.