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Over recent decades, the number of floodplain restoration projects has increased worldwide. In Switzerland, several projects have been implemented to maintain or recreate ecological functions of floodplains. Despite this, little is known about the potential of floodplain soils to release and/or accumulate carbon. In alluvial soils, carbon storage is strongly influenced by fluvial dynamics, and therefore a better understanding of carbon fluxes and stocks in such settings is clearly needed. To evaluate the impact of river restoration on carbon storage in alluvial soils, we aimed to quantify and explain carbon storage and soil organic matter (SOM) stabilisation in the uppermost soil humic layer. Three floodplains were investigated showing each of them different levels of human disturbance: a near-natural section along the Rhine River, and both restored and embanked sections along the Thur River and Emme River. Carbon storage was determined by total organic carbon (TOC) stocks. SOM stabilisation was evaluated by considering the TOC content in different granulometric fractions (1000–2000 μm, 500–1000 μm, and 250–500 μm) and the macro-aggregate formation, i.e. the abundance of water-stable aggregates (WSA) and the mean weight diameter of macro-aggregates (MWD). Our results show that the carbon storage and SOM stabilisation parameters were all related to soil properties such as clay, silt and total iron contents of the upper humic layer. Within each floodplain, carbon storage and SOM stabilisation parameters differed according to soil profile groups, thus reflecting a soil gradient evolution from bare alluvium soils to more stabilised soils and a hydric functioning (soils with hydromorphic features). In addition, river restoration showed various impacts on carbon storage and SOM stabilisation parameters depending on the floodplains, with a significant difference between embanked and restored sections for the Emme floodplain and no difference for the Thur floodplain.