Floodplains are among the most important long-term terrestrial carbon sinks, yet the controls governing millennial-scale carbon accumulation remain poorly constrained, particularly in large fluvial systems. Here we reconstruct the history of organic carbon accumulation in the Lower Danube Floodplain (LDF), one of the largest floodplain systems in Europe, using stratigraphic and chronological data from eight sediment cores spanning the last 7000 years. Total organic carbon (TOC), grain-size distribution, dry bulk density, and sedimentation rates derived from Bayesian age–depth models were integrated to quantify temporal changes in carbon accumulation rates (CAR) and to evaluate the geomorphic and environmental controls governing long-term carbon burial.</p> <p>Over the investigated period, large volumes of sediment accumulated across the LDF, forming a thick stratigraphic sequence that stores substantial amounts of organic carbon. However, long-term carbon burial did not occur at a constant rate but instead reflects three distinct phases controlled by changing boundary conditions. During the early part of the record, rapid floodplain aggradation associated with post-glacial base-level rise promoted efficient carbon burial through accelerated mineral sediment deposition despite relatively low organic carbon concentrations. Following base-level stabilization, sedimentation rates declined and the system shifted toward preservation-dominated sequestration, characterized by higher organic carbon contents but lower carbon accumulation efficiency under more stable hydrogeomorphic conditions. During the last two millennia, increasing human activity in the Danube basin enhanced sediment delivery, leading to a renewed increase in carbon burial despite declining organic carbon concentrations.</p> <p>Superimposed on these millennial-scale trends, carbon burial also varies substantially among sedimentary facies, reflecting contrasting depositional environments and carbon sequestration mechanisms within the floodplain. Facies-based analyses reveal contrasting mechanisms of carbon storage across floodplain environments. Peat and organic-rich deposits exhibit the highest TOC values (average 17 %) but relatively moderate CAR due to low sediment accumulation rates, whereas paleochannel and overbank deposits achieve higher CAR through rapid burial of mineral sediments containing lower organic carbon concentrations. These results demonstrate that long-term floodplain carbon sequestration is governed by the interaction between accommodation space, sedimentation rate, and hydrological connectivity rather than organic carbon concentration alone.</p> <p>These findings highlight the importance of maintaining hydrological connectivity and sediment delivery in order to sustain carbon burial in large floodplain systems, suggesting that restoration strategies focused on reconnecting floodplain surfaces to fluvial processes may enhance long-term carbon sequestration and associated ecosystem services.