Aquaculture ponds play an important role in the global carbon cycle. In order to understand the dynamics of carbon in the shrimp ponds, dissolved carbon (dissolved organic carbon[DOC] and dissolved inorganic carbon[DIC]) concentrations in the pond water column, and the exchange fluxes of dissolved carbon across the sediment-water interface, were investigated in the Min River estuary (MRE) and Jiulong River estuary (JRE) on the southeast coast of China. Water and sediment samples were collected using a hydrophore and sediment sampler from three shrimp ponds in June, August, and October 2015, respectively. Meanwhile, water-quality indicators (water temperature, pH, dissolved oxygen, and salinity) were measured in situ using a portable instrument. The dissolved carbon concentration in water was analyzed using a SHIMADZU TOC-V_CPH/CPN analyzer. Sediment oxygen and nutrient exchange (SONE) incubation techniques were used to measure the rates of dissolved carbon fluxes. The results showed that dissolved carbon concentrations in the pond water, and fluxes across the sediment-water interface from the estuaries of shrimp ponds greatly varied in spatial and seasonal dynamics. Mean dissolved carbon concentrations and fluxes were significantly higher from the shrimp ponds in the Min River estuary than in the Jiulong River estuary (P < 0.05). Average seasonal dissolved carbon concentrations (or fluxes) in the Min River estuary and Jiulong River estuary followed the order:August > October > June and October > August > June, respectively. The variations in dissolved carbon concentrations in the water were significantly positively correlated with the dissolved carbon fluxes across the sediment-water interface, indicating that the process of dissolved carbon release in the sediment affects the dynamic variation of dissolved carbon concentrations in the water column. Overall, the dynamic variation of dissolved carbon concentrations and fluxes in the shrimp ponds could be due to the synthetic action of abiotic factors (e.g., temperature and salinity), the foraging and metabolic activity of shrimp, and feed supply. Our study highlights the need to consider the spatio-temporal difference of carbonic biogeochemical cycles to better understand the dynamic of carbon cycling from the aquaculture ecosystems in the estuaries.