In order to understand the impact of hydrological changes of the Amazon River on sedimentary organic matter (OM) composition in Amazonian floodplain lakes, three sediment cores were collected from Lake Maracá (eastern Amazonia) along a transect from the Amazon River main channel to inland. The cores were dated with 14C accelerator mass spectrometry (AMS) and studied by x-ray, mineralogical composition, total organic carbon (TOC) and total nitrogen (TN) contents, stable isotopic composition of TOC and TN (δ13COC and δ15N) and glycerol dialkyl glycerol tetraether (GDGT) distributions. Two distinctive sedimentary depositional phases were identified based on the mineralogical composition and the geochemical characteristics of sedimentary OM. During the early-mid Holocene (~13,000-3200 cal. yr BP), low values of TOC followed by a break in sedimentation suggest a complete drying of the lake caused by drier climatic conditions. Between 3600 and 3200 cal. yr BP, this lake received a reduced influence of the Amazon River main stem. This induced a predominant deposition of C3-plant-derived OM supplied by surface erosion and runoff of acidic soil. A distinct connection of Lake Maracá to the Amazon River began after 3200 cal. yr BP and became permanently established, with its modern characteristics, at 1880 cal. yr BP. This change provoked an increased contribution of phytoplankton and semi-aquatic C4 macrophytes as well as C3 plant derived more alkaline soil OM to the sedimentary OM pool. Consequently, our study demonstrates that the source of sedimentary OM in the Amazon floodplain lakes was strongly linked to the Amazon River hydrodynamics during the late Holocene. © The Author(s) 2013.