In this study, we investigated the seasonal and spatial pattern of sedimentary organic matter (SOM) in five floodplain lakes of the central Amazon basin (Cabaliana, Janauaca, Canaçari, Mirituba and Curuai) which have different morphologies, hydrodynamics and vegetation cover-ages. Surface sediments were collected in four hydrological seasons: low water (LW), rising water (RW), high water (HW) and falling water (FW) in 2009 and 2010. We investigated commonly used bulk geochemical tracers such as the C : N ratio and the stable isotopic composition of organic carbon (δ 13 C org). These results were compared with lignin phenol parameters as an indicator of vascular plant detritus and branched glycerol dialkyl glycerol tetraethers (brGDGTs) to trace the input of soil organic matter (OM) from land to the aquatic settings. We also applied the crenarchaeol as an indicator of aquatic (rivers and lakes) OM. Our data showed that during the RW and FW seasons, the surface sediments were enriched in lignin and brGDGTs in comparison to other seasons. Our study also indicated that floodplain lake sediments primarily consisted of allochthonous, C 3 plant-derived OM. However, a downstream increase in C 4 macrophyte-derived OM contribution was observed along the gradient of increasing open waters-i.e., from upstream to downstream. Accordingly , we attribute the temporal and spatial difference in SOM composition to the hydrological dynamics between the floodplain lakes and the surrounding flooded forests.