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Floodplains are vital components of river ecosystems and play an important role in carbon cycling and storage at catchment and global scales. For efficient river management and conservation, it is critical to understand the functional role of spatiotemporally complex and dynamic habitat mosaics of river floodplains. Unfortunately, the fundamental understanding of mineralization and carbon flux patterns across complex floodplains is still fragmentary. In this study, respiratory potential (i.e., electron transport system activity [ETSA]) was quantified seasonally across different aquatic and terrestrial habitats (wetted channels, gravel bars, islands, riparian forests, and grasslands) of 2 Alpine floodplains differing in climate, altitude, discharge, flow alteration intensity, and land use (Soca [natural flow regime, 12% grassland area] and Urbach [mean annual discharge reduction by 30% due to water abstraction, 69% grassland area]). In situ respiration (R) was measured, and ETSA-R ratios were calculated to examine differences in exploitation intensity of the overall respiratory capacity among floodplain habitats and seasons. ETSA and R provided potential and actual estimates, respectively, of organic matter mineralization in the different floodplain habitats. Hierarchical linear regression across habitat types showed that organic matter, grain sizes <0.063 mm, and water content were the most important predictors of ETSA in both floodplains, and grain sizes 2-0.063 and >8mm were also highly important for the Soca floodplain. The combination of ETSA and R measurements conducted in contrasting floodplains increased our understanding of the relationships between floodplain habitat heterogeneity, organic matter mineralization and human impacts, that is, structural-functional linkages in floodplains. These data are integral towards predicting changes in floodplain function in response to environmental alterations from increasing human pressures and environmental change.