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Human activities have increased anthropogenic CO2 emissions, which are believed to play important roles in global warming. The spatiotemporal variations of CO2 concentration and flux at fine spatial scales in aquaculture ponds remain unclear, particularly in China, the country with the largest aquaculture. In this study, the plot-scale spatiotemporal variations of water CO2 concentration and flux, both within and among ponds, were researched in shrimp ponds in Shanyutan Wetland, Min River Estuary, Southeast China. The average water CO2 concentration and flux across the water-air interface in the shrimp ponds over the shrimp farming period varied from 22.79 +/- 0.54 to 186.66 +/- 8.71molL(-1) and from -0.50 +/- 0.04 to 2.87 +/- 0.78molm(-2)day(-1), respectively. There was no remarkable difference in CO2 concentration and flux within the ponds, but significantly spatiotemporal differences in CO2 flux were observed between shrimp ponds. Chlorophyll a, pH, salinity, air temperature, and morphometry were the important factors driving the spatiotemporal patterns of CO2 flux in the shrimp ponds. Our findings highlighted the importance and spatiotemporal variations of CO2 flux in the important coastal ecosystems.