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Floodplain soils are important reservoirs of organic carbon (OC) in the terrestrial carbon cycle. Few rivers and floodplains in the world and particularly in central Europe are in a natural state. They are regulated, stabilised from erosion behind artificial levees, drained and used for agriculture. Fluvisols store high amounts of OC from the topsoil to the subsoil, but little is known about the soil organic matter (SOM) quality and its vulnerability to decomposition. In this study, two regulated floodplains originating from different parent materials under grassland use in Southern Germany (Alpine Foreland and the Bavarian Forest) were sampled and analysed for the quantity and quality of inherent SOM in the topsoil and two subsoil levels. We characterised bulk soil (pH, texture, inorganic carbon and total nitrogen) and applied a combined density and size fractionation scheme to obtain six fractions. The chemical composition of the fractions was further determined using solid-state C-13 NMR spectroscopy (SOM composition), as well as X-ray diffraction (clay mineralogy) and N-2-BET (specific surface area (SSA)). Contributions of light fractions and especially of occluded particulate organic matter (oPOM(fine)) to the total OC were remarkably high in the subsoils. Organo-mineral associations (OMFfine) highly contributed to total OC at both sites but only in the topsoils. The highest OC concentrations of OMFfine were found in calcareous parent material, which shows that polyvalent cations promote OC storage. However, the inter-site as well as intra-site heterogeneity of oPOM(fine) and OMFfine OC contribution was highly variable. In the Bavarian Forest, oPOM(fine) was enriched in lipids in the subsoil. This was most probably due to a limited supply of oxygen in the aggregates through fluctuating groundwater levels that retarded decomposition and selectively preserved aliphatic compounds. In the Alpine Foreland, soil biota had mixed fresh SOM into the subsoil. There, oPOM(fine) contained all the functional C-groups, particularly carbohydrates. A changing global climate jeopardises OC reservoirs in floodplains, due to increased flooding and associated river bank erosion. Such disturbances not only cause losses of productive land but also release OC stored in light fractions that could be oxidised to CO2, depending on its chemical composition, thus adding to global warming.