The semi-arid Amboseli landscape, southern Kenya, is characterised by intermittent groundwater-fed wetlands that form sedimentary geoarchives recording past ecosystem changes. We present a 5000-year environmental history of a radiocarbon dated sediment core from Esambu Swamp adjacent to Amboseli National Park. Although radiocarbon dates suggest an unconformity or sedimentary gap that spans between 3800 and 500 cal year BP, the record provides a unique insight into the long-term ecosystem history and wetland processes, particularly the past 500 years. Climatic shifts, fire activity and recent anthropogenic activity drive changes in ecosystem composition. Prior to 3800 cal year BP the pollen data suggest semi-arid savanna ecosystem persisted near the wetland. The wetland transgressed at some time between 3800 and 500 cal year BP and it is difficult to constrain this timing further, and palustrine peaty sediments have accumulated since 400 cal year BP. Increased abundance of Afromontane forest taxa from adjacent highlands of Kilimanjaro and the Chyulu Hills and local arboreal taxa reflect changes in regional moisture budgets. Particularly transformative changes occurred in the last five centuries, associated with increased local biomass burning coeval with the arrival of Maa-speaking pastoralists and intensification of the ivory trade. Cereal crops occurred consistently from around 300 cal year BP, indicative of further anthropogenic activity. The study provides unique insight in Amboseli ecosystem history and the link between ecosystem drivers of change. Such long-term perspectives are crucial for future climate change and associated livelihood impacts, so that suitable responses to ensure sustainable management practices can be developed in an important conservation landscape.Electronic supplementary materialThe online version of this article (10.1007/s13280-018-1014-2) contains supplementary material, which is available to authorized users.