Amazonian peatlands are carbon dense ecosystems which also contribute to the biological diversity of the western Amazon. Their existence remained unconfirmed until scientific studies in the last decade revealed extensive peatlands in the Pastaza-Marañón basin of Peru. This study sought to investigate the palaeoecological history and hydrological behaviour of peatlands in the Pastaza-Marañón basin. The aims of the study were to determine the key drivers of past vegetation change in two Amazonian peatlands, to produce the first explicit conceptual model of Amazonian peatland development, to improve our understanding of the hydrological behaviour of Amazonian peatlands, and to improve interpretations of the late Quaternary tropical pollen record. Field data were collected in order to determine the saturated hydraulic conductivity (K), an essential parameter for hydrological models, in three Amazonian peatlands. Measured K at 50 cm depth varied between 0.00032 and 0.11 cm s-1, and at 90 cm, it varies between 0.00027 and 0.057 cm s-1. Simulations using a simple hydrological model suggest that under current climatic conditions, even with high K, peatlands would be unable to shed the large amount of water entering the system via rainfall through subsurface flow alone. An annual record of water table variation from one site, Quistococha, shows that the water level can fall rapidly (c. 1.6 cm d-1) in the absence of rainfall. The main conclusions to be drawn from this part of the study are that most of the water leaves these peatlands via overland flow and/or evapotranspiration, and that regular rainfall is essential for maintaining the moist conditions necessary for continued peat accumulation. Palaeoecological data were collected from two peatlands: Quistococha and San Jorge. The data from Quistococha constitute the first multiple-core study of an Amazonian peatland, and form the basis of a developmental model. These data show that a well-placed single core can represent the main vegetation changes, although multiple cores add valuable detail to the picture of site development. Lateral growth mostly occurred through ‘primary mire formation’, where peat begins accumulating simultaneously across a site: the expansion of Quistococha therefore differs from many temperate and sub-arctic peatlands, where primary mire formation is mostly confined to coastal areas. Differences in the subsurface topography are shown to have affected vegetation development, and likely resulted in higher beta diversity than present during the early stages of Quistococha’s development. At San Jorge, radiocarbon dating has revealed a period of slow accumulation between 1300 and 450 cal yr BP which is also associated with a major change in vegetation from a Pistia dominated aquatic pollen assemblage to a Mauritia and Mauritiella dominated palm swamp assemblage. This is amongst the first evidence suggesting an effect of late-Holocene climatic change on ecosystems in the western Amazon, but will require confirmation through further work at other sites in the region.