Holocene environments have been reconstructed by sedimentological, mineralogical and organic geochemical analysis of a 270-cm core from Santa Ninha Lake, a floodplain lake in lower Amazonia. Dated by fourteen AMS-radiocarbon dates, the sediment core has a basal age of 5,600 cal years BP and different sedimentary units were identified. These units document various hydrologic phases in the evolution of this lake. Reduced Amazon River influence, with reduced high-water levels of the river, characterized the period between 5,600 and 5,100 cal years BP. Comparison with other Amazonian and Andean paleoclimate studies point to a dryer climate during this phase. After 5,100 cal years BP coarse sediments and quartz increase which suggest a higher inflow of the Amazon River. Between 5,000 and 2,300 cal years BP the coarse sediments and quartz remain high but the organic carbon showed the lowest values. The riverine inflow caused dilution of the organic material produced in the lake and consequently low rates of carbon flux in these phases were recorded. These results show that the hydrodynamics of the Amazon River strongly influence the behavior, productivity and consequently the sedimentation process in the floodplain lakes.