<p>Inland waters cover only a small fraction of the global surface area. However, high carbon burial rates can potentially contribute to the carbon sinks of inland wetlands. Recently, many inland waters have been converted to freshwater aquaculture to meet the rising food demand of a growing human population. However, the changes in the carbon balance of these freshwater aquaculture ponds have not been examined. In this study, we constructed in situ carbon budgets for freshwater ponds with and without Asian clam (<i>Corbicula fluminea</i>) culture in eastern Taiwan. All the clam culture ponds acted as carbon sources (0.109 to 0.188&#xa0;g C m⁻² d⁻¹), whereas the pond without clams acted as a carbon sink (− 0.378&#xa0;g&#xa0;C m⁻² d⁻¹). This shift in the carbon balance may be attributed to CO₂ efflux resulting from shell growth via calcification. This study presents the first carbon budget for freshwater aquaculture ponds, which can be further applied to other farming animals to better understand the impact of aquaculture on the carbon balance of inland waters.</p>