Lake carbon (C) cycling is a key component of the global C cycle and associated C source and sink processes. The partial pressure of carbon dioxide (pCO2) and carbon dioxide (CO2) exchange flux at the lake-air interface (Fc) are controlled by complex physical, chemical, and biological mechanisms. It would be instructively significant to determine whether hydrological processes drive conversion shifts between C sources and sinks in floodplain-lake systems. Findings from this study show that exogenous input and in situ metabolism related to photosynthesis, respiration, and organic matter degradation were the main driving mechanisms of CO2 absorption and release in a large floodplain-lake system (i.e., Lake Poyang). Moreover, the intense and frequent water-level fluctuations inherent to floodplain-lakes may also have a direct or indirect impact on C cycling processes and CO2 exchange rates in floodplain-lake systems via their effect on physical processes, inorganic C transport, in-situ metabolic processes. We confirmed the potential of C source and sink conversion in floodplain-lakes under hydrological fluctuations, and strengthen the understanding of driving mechanisms of C source and sink conversion in floodplain systems.