A mesocosm study was carried out to determine whether flooding affected soil microbial structure and function. Over a 24 day period soils were either flooded or remained dry and changes in the microbial community structure, microbial metabolic activity (determined by looking at soil respiration rates and exo-enzyme activity), community level physiological profiles and soil carbon speciation were examined. Flooding induced significant changes in the microbial community structure and increased soil respiration and enzymatic degradation rates. Shifts occurred in carbon speciation after flooding and increases in ‘labile’ carbon fractions were observed. The duration of flooding was also important for carbon dynamics and microbial community structure. Based on the results of the mesocosm experiment a conceptual model of floodplain soils response to flooding over time was formulated. The findings of this mesocosm study illustrate the importance of flooding to floodplain soil functioning. Copyright © 2010 John Wiley & Sons, Ltd.