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In the Miocene , a large wetland system extended from the Andean foothills into western Amazonia. This system has no modern analogue and the driving mechanisms are not yet fully understood. Dynamic topography and Andean uplift are thought to have controlled deposition, with allocyclic base level changes driven by eustasy and orbital forcing also playing a role. In this study we investigate the presumed orbital cyclicity that controlled sediment deposition, while also assessing sediment source and biomes in the Miocene wetland. We do this by integrating lithological, palynological, malacological and geochemical data from the Los Chorros site (Amazon River, Colombia), and by placing our data in a sequence stratigraphic framework. In this sequence biostratigraphic evaluation, the Los Chorros succession is visualized to be composed of a series of flood-fill packages, with a rapid initial flood, marine-influenced conditions at the time of maximum flood, followed by a longer regressive infill phase. Based on the palynology we could differentiate local vegetation, such as palm swamps, from regional origin such as terra firme vegetation (non-flooded Amazonian forest) and Andean montane forest, while from sediment geochemistry we could separate local and regional sediment sources. At the times of flooding, oligotrophic and eutrophic aquatic conditions alternatively characterized the wetland, as is shown by the presence of algae, floating ferns, and mollusc assemblages, while intervening subaquatic debris points to proximal submerged lowlands. In the lower 20 m of the section, marine influences are intermittently evident and shown by short-lived maxima of mangrove pollen, foraminiferal test linings, dinoflagellate cysts , coastal mollusc species, and an episodic decline in terrestrial biomarkers. The upper 5 m of the section is characterized by floodplain forest taxa with a diversity in tropical rain forest taxa and relatively few lacustrine indicators. These marine, mangrove, and lacustrine indicators suggest that the outcrops at Los Chorros represent predominant marine-influenced lacustrine conditions during periods of sea level highstand . The sequence biostratigraphic evaluation further points to eight 41 kyr obliquity-driven depositional cycles, with rapid phases of transgression. Mangrove elements would have colonised within the timeframe of each sea level rise . Based on this relative age constraint and comparison to regional records, deposition likely took place prior to the 13.8 Myr global sea level fall, and most likely during the period just after 14.5 Ma, between Middle Miocene Climatic Optimum (MMCO; 17–14 Ma) and Middle Miocene Climate Transition (MMCT; 14.7–13.8 Ma). Palynological evidence further suggests that to the west, surface elevation ranged from ~1000 up to ~3500 m and hosted protoparamo vegetation, the oldest yet reported and in agreement with predictions from molecular studies. In contrast, contemporaneous sites to the northeast of the wetland consisted of fluvial and cratonic formations, as shown by their Nd and Sr isotopic sediment signature. In summary, our data lead to an improved understanding of how geological and astronomical mechanisms controlled the floral and faunal distribution and controlled sediment deposition in western Amazonia during the middle Miocene. As Miocene conditions strongly contrast with modern western Amazonia, our data provide an important context for the deep time history and evolution of the modern western Amazon rainforest.