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Temporary rivers are characterized by recurrent dry phases, and global warming will stress their hydrology by amplifying extreme events. Microbial degradation and transformation of organic matter (OM) in riverbed sediment are key processes with regard to carbon and nutrient fluxes. In this study, we describe structural and functional changes of benthic microbial communities in a riverine environment subject to hydrological fluctuation. Sampling was carried out in the outlet section of the Mulargia River (Sardinia, Italy) under various water regimes, including one flood event. Overall, sediments were characterized by low bacterial cell abundance (range 0.6-1.8 x 10(9) cell g(-1)) as a consequence of their low nutrient and OM concentrations. No major differences were found in the community composition. Alpha-Proteobacteria dominated during the whole year (range 21-30%) followed by Beta-Proteobacteria, Gamma-Proteobacteria, and Cytophaga-Flavobacteria which always contributed < 18%. Planctomycetes and Firmicutes were found in smaller amounts (< 7%). In spring, when the highest total organic carbon content was also detected (0.42% w/w), both bacterial abundance and C production (BCP, 170 nmol C h(-1) g(-1)) reached relatively high values. During the flood event, an increase in BCP and the highest values of community respiration (CR, 74 nmol C h(-1) g(-1)) were observed. Moreover, most of the extracellular enzyme activities (EEA) changed significantly during the flood. The variation of the water flow itself can explain part of these changes and other factors also come into play. The presence of different patterns of functional parameters could suggest that the quality of the OM could be the major driving force in nutrient flux.