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Soil C is a key factor influencing soil health and, by inference, ecosystem condition. In arid and semi-arid regions, soil moisture limits accumulation and decomposition of soil C. On floodplains, soil moisture can come from rainfall events or periodic flooding. The effect of flooding on soil C decomposition has received some attention in the literature but mostly through the study of agricultural systems or mesocosms. Field studies of actual floods are not common. We measured soil C response to a managed flood on a semi-arid lowland river floodplain in southeastern Australia before and after inundation at control (unflooded), floodplain (low hydraulic energy), and flood runner (high hydraulic energy) sites. At control sites, soil C changed little from before to 16 d after the onset of the flood. At flooded sites, most measures of soil C (total soil organic matter [floodplain sites only], permanganate-oxidizable C, persulfate-extractable C, water-extractable C [flood runner sites only], microbial C, and root material) were lower 16 d after than before the flood. However, the activity of key hydrolytic exo-enzymes associated with soil C decomposition did not change. Following the initial decline in soil C at the flooded sites, soil properties remained essentially constant for the remainder of the flood. Upon flood recession, slight increases in C pools occurred at the flood runner site (possibly associated with the formation of debris dams) but not at the floodplain or control sites. The changes in soil C pools after flood recession were at least an order of magnitude lower than those observed at the same location during more extended flooding. We argue that the loss of soil C associated with short-duration floods may adversely affect ecosystem condition of lowland river floodplains. Managed floods should be of long enough duration (months) to promote the growth of submerged and emergent aquatic macrophytes on the floodplain because aquatic macrophyte production is an important source of soil C after flood recession in lowland river floodplains.