Floodplain deposition rates have increased markedly under influence of human impact throughout the late Holocene in many western and central European catchments. Consequently the geomorphology and ecology of many floodplains changed. In this study we discuss this human impact and its influence on the floodplain geoecology during the middle and late Holocene for the headwaters of the Dijle catchment, located in the Belgian loess belt. The floodplain geoecology and the regional vegetation was reconstructed from sedimentological and palynological analyses. An age–depth model for the studied sequences was obtained using 17 radiocarbon dates. Statistical analyses of the pollen data (cluster analysis and canonical correspondence analysis) were used to detect changes in the pollen record. Our data show that until c. 2500 cal. BP, human impact was nearly absent or localized with no discernible influence on the floodplain geoecology. The floodplain was in a stable phase and consisted of a marshy environment where organic material could accumulate, which is interpreted as the natural state of the floodplain. From c. 2500 cal. BP onwards, human impact gradually increased. However, only when human impact in the catchment crossed a threshold around 500 cal. BP, the floodplain geoecology changed with clearing of the Alder carr forest, the establishment of a single channel river and the dominance of minerogenic overbank sedimentation. Spatial variability in the coupling between increasing human impact and changes in floodplain geoecology can be attributed to differences in hillslope–floodplain connectivity and local differences in human impact.