The largest areas of white‐sand vegetation in northern Amazonia are confined to Late Pleistocene–Holocene megafan depositional systems, which suggest a relationship between the two. The aim of this work is to determine: (i) the relative role of sedimentary history and recent ecological processes to explaining the mosaic of white‐sand forest patches, grasslands and shrublands in a wetland area of northern Amazonia; and (ii) the long‐term successional trajectory that led to the establishment of the white‐sand forest patches. Facies analysis was used to reconstruct the megafan paleoenvironment; δ¹³C, total organic carbon and carbon/nitrogen from sedimentary organic matter to reconstruct the past vegetation; and floristic inventories to characterize the modern vegetation. The results revealed that the Viruá megafan consists of various sandy sub‐environments, including aeolian sand dunes and sheets developed mostly in the Holocene after the megafan turned inactive as a depositional site. Dune margins and tops are colonized by white‐sand trees mixed with a few generalist rain‐forest species, whereas adjacent lower‐lying areas, which are affected by seasonal flooding, are covered by graminoid plants and/or shrubs. The latter initiated their development over the megafan surface in different times of the Holocene due to hydrological gradients imposed by the topography of the various megafan depositional environments, while the white‐sand forest became dominant only on sand dunes over the last few centuries. We suggest that the late Quaternary sedimentary history was crucial in creating morphologies that now determine topographic gradients responsible for different vegetation physiognomies over the Amazonian lowlands.