Due to their spatial complexity and dynamic na- ture, floodplains provide a wide range of ecosystem func- tions. However, because of flow regulation, many river- ine floodplains have lost their characteristic heterogeneity. Restoration of floodplain habitats and the rehabilitation of key ecosystem functions, many of them linked to organic carbon (C) dynamics in riparian soils, has therefore become a major goal of environmental policy. The fundamental un- derstanding of the factors that drive the processes involved in C cycling in heterogeneous and dynamic systems such as floodplains is however only fragmentary. We quantified soil organic C pools (microbial C and wa- ter extractable organic C) and fluxes (soil respiration and net methane production) in functional process zones of ad- jacent channelized and widened sections of the Thur River, NE Switzerland, on a seasonal basis. The objective was to assess how spatial heterogeneity and temporal variability of these pools and fluxes relate to physicochemical soil proper- ties on one hand, and to soil environmental conditions and flood disturbance on the other hand. Overall, factors related to seasonality and flooding (tem- perature, water content, organic matter input) affected soil C dynamics more than soil properties did. Coarse-textured soils on gravel bars in the restored section were character- ized by low base-levels of organic C pools due to low TOC contents. However, frequent disturbance by flood pulses led to high heterogeneity with temporarily and locally increased C pools and soil respiration. By contrast, in stable riparian forests, the finer texture of the soils and corresponding higher TOC contents and water retention capacity led to high base- levels of C pools. Spatial heterogeneity was low, but major floods and seasonal differences in temperature had additional impacts on both pools and fluxes. Soil properties and base levels of C pools in the dam foreland of the channelized sec- tion were similar to the gravel bars of the restored section. By contrast, spatial heterogeneity, seasonal effects and flood dis- turbance were similar to the forests, except for indications of high CH4 production that are explained by long travel times of infiltrating water favoring reducing conditions. Overall, the restored section exhibited both a larger range and a higher heterogeneity of organic C pools and fluxes as well as a higher plant biodiversity than the channelized section. This suggests that restoration has indeed led to an increase in func- tional diversity.