Small-scale aquaculture operation is being increasing practised around the world, particularly in the developing countries, but the greenhouse gas (GHG) dynamics and fluxes from small aquaculture ponds are still poorly assessed. In this study, the dissolved concentrations and fluxes of CO2 and CH4 were determined in three coastal earthen shrimp ponds over one whole year, covering both the farming and non-farming periods, in the Min River Estuary, southeastern China. Both ebullitive and diffusive CH4 fluxes were measured, which were rarely done in previous studies. The average concentrations of dissolved CO2 and CH4 in water column in the farming period varied between 18.1 +/- 0.1 and 79.6 +/- 1.1 mu mol L-1, and 1.3 +/- 0.1 and 55.9 +/- 3.2 mu mol L-1, respectively. When averaged across the whole year, the mean CO2 and CH4 fluxes from the ponds were - 18.4 +/- 7.4 and 22.6 +/- 6.9 mg m- 2 h-1, respectively, suggesting that the shrimp ponds acted as a CO2 sink and a CH4 source. Based on the sustained-flux global warming potential (SGWP) and sustained-flux global cooling potential (SGCP) models, the annual warming potential was estimated to be 7.1 x 103 g CO2-eq m- 2 yr- 1, with approximately 90% of this arising from the farming period. Ebullition was the dominant emission pathway for CH4, accounting for over 90% of the total CH4 emission during the farming period. This full-year study improves our understanding of carbon cycling in coastal aquaculture ponds and provides a scientific basis for updating the GHG inventories.