A synthesis of the impacts of the Amazon River hydrological changes on the sedimentation process of organic matter (OM) in three different floodplain lakes (Santa Ninha, Maracá, and Comprido lakes) is presented in this study. Today the Santa Ninha and Maracá lakes are directly and permanently connected with the main channel of the Amazon River, in contrast to Comprido Lake, which is indirectly and periodically influenced by the Amazon River due to its greater distance from the main channel. All three lake sediment records showed a reduced river inflow due to dry climatic conditions during the early and middle Holocene followed by an increased fluvial input during the wetter late Holocene. In Santa Ninha and Maraca Lakes, the reduced river inflow period was recorded by sediments with a low abundance of smectite (on average ~20wt.%), a clay mineral mainly transported by the fluvial system, high total organic carbon (TOC) contents (on average ~8.2wt.%), and a predominantly acidic soil OM input evidenced by high concentrations (on average 180μggTOC-1) of branched glycerol dialkyl glycerol tetraethers (GDGT). During the late Holocene, a higher smectite abundance (on average ~43 wt.%) and a lower TOC content (on average ~1.4 wt.%) pointed to greater dilution by riverine lithogenic matter. This change was accompanied by a proportional increase in the aquatically produced crenarchaeol, suggesting a higher lake water level. In Comprido Lake, a sedimentation gap occurred during the early and middle Holocene. The wetter late Holocene, since 3000calyears BP, was characterized by high TOC values (on average ~9wt.%) and a sharp increase in soil OM input as recorded by an increase in branched GDGT concentrations (on average ~81μggTOC-1), but the smectite content was low (on average ~14%). This combination suggests that the soil OM input to Comprido Lake from the local catchment area became dominant during the wet-climate late Holocene due to the large distance of the lake from the Amazon River main channel. Consequently, our study shows that the sedimentation processes of OM in Amazonian floodplain lakes were strongly influenced by variations in the hydrodynamic regime of the Amazon River during the Holocene. However, the impacts of the variations on the three floodplain lakes were different depending on the distance of each lake from the main channel of the Amazon River.