Coastal wetlands store large amounts of soil organic carbon (SOC), however, little is known on SOC stabilization mechanisms (e.g. aggregation or mineral-association) in these ecosystems. In estuarine marshes, SOC storage is dominated by a complex interaction of abiotic conditions such as tidal inundation or salinity with biotic ecosystem components, leading to strong spatio-temporal variations within and between estuaries. Our aim was to assess (i) SOC stocks, (ii) SOC stabilization mechanisms, and (iii) their environmental drivers along estuarine gradients. We analyzed topsoil (0-10 cm) and subsoil (10-30 cm) samples from three marsh zones representing three flooding regimes (daily, monthly, yearly) in three marsh types along the salinity gradient (salt, brackish, freshwater) of the Elbe Estuary, Germany. Total SOC stocks, as well as SOC density fractions were analyzed and related to site characteristics (soil texture, soil pH, redox conditions, aboveground plant biomass). Increasing salinity and flooding frequency negatively affected SOC stocks in 0-30 cm (9.3-74.6 t ha-1). This was related to plant biomass and soil texture along the estuary. Mineral-associated OC (CMAOM) was the largest SOC fraction (59% of total SOC), followed by OC in aggregates (CoPOM) (24%) and OC in free particulate organic matter (CfPOM) (16%). The CMAOM amount in topsoils decreased downstream with increasing salinity, reflecting decreasing fine-texture along the estuary. The amount of CoPOM was higher in topsoils and less flood-affected marshes, indicating negative effects of flooding on aggregation. The relative proportion of CfPOM to total SOC increased with increasing flooding frequency and correlated positively with reducing soil conditions but not with the local plant biomass. Our results underline the importance of estuarine gradients as drivers of SOC storage and stabilization. Climate-change induced sea-level rise and variations in salinity might threaten SOC stocks and hamper SOC stabilization in estuarine soils.