Soil microbial communities are the most active components in the riparian biota, and are critical in driving carbon cycling. The periodic flooding in riparian zones is a primary driving force in the changes of soil microbial community structures and function. However, whether such events can induce changes in microbial carbon metabolism efficiency has not been fully revealed, especially in large reservoirs that experience counter-seasonal water level fluctuations (WLFs). In this study, high-throughput sequencing and the