This study investigates Holocene floodplain evolution and flooding phases as experienced in the Lower Meuse catchment, primarily based on grain-size distributions of channel-fill and floodplain deposits in sediment cores. The presence of post-depositional Fe[sbnd]Mn concretions and resistant organic particulate materials impedes the direct use of grain-size data. By combining end-member modelling results with laboratory observations, we have constructed a Flood Energy Index (FEI), which allows identification of phases of past increased flooding from the grain-size signal. Since concretions and organic-rich sediments regularly occur in floodplain sediments, we emphasize that the quality of a grain-size dataset should be assessed prior to its use for reconstruction of flood events. We suggest that the new approach has potential to become standardized within paleoflood research. The temporal variation of FEI in Meuse sediment cores highlights multi-centennial flooding phases occurring at c. 8500, c. 8000, c. 7600, c. 7000 and c. 5900 cal BP within the fluvio-lacustrine environment (early–middle Holocene). The record of low flood activity in the Subboreal is attributed to a cooler and dryer climate anomaly after the Holocene Climatic Optimum. In the late Holocene, the first flooding phase occurring at c. 2800 cal BP can be linked to the 2.8 ka climate anomaly. During the last two thousand years, the variation of FEI index reveals oscillating flood regimes in the Lower Meuse floodplain. The last three recorded flooding phases most likely coincide with the Roman Period (c. 12 BCE–250 CE), the Medieval Warm Period (c. 950–1400 CE) and the Little Ice Age (c. 1400–850 CE). Despite uncertainty in the age-model, the rapid accumulation rate and amplified flood magnitudes imply increased fluvial instability during the late Holocene, indicating that humans exerted a profound influence on fluvial dynamics in the Meuse.