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Aquaculture ponds are potentially large sources of atmospheric methane (CH4) that can exacerbate climate change. A thorough understanding of various CH4 biogeochemical processes occurring in the ponds is essential for the prediction and management of CH4 emissions arising from aquaculture. However, the variations in pond CH4 biogeochemical processes among estuaries and aquaculture stages remain poorly understood. In this study, we assessed the net sediment release, oxidation, and dissolved concentrations of CH4 in aquaculture ponds in two subtropical estuaries among three shrimp growth stages in Southeast China. Overall, porewater CH4 concentrations and sediment CH4 release rates varied greatly among different stages in the order: middle stage > final stage > initial stage. Water column CH4 concentrations and overlying water CH4 oxidation rates showed an increasing trend over the study period. Sediment CH4 release rates and dissolved CH4 concentrations also varied considerably between the two estuaries. In the more saline Jiulong River Estuary, sediment CH4 release rate was lower while the shrimp survival rate and yield were higher as compared to the Min River Estuary with a lower water salinity. Our results suggest that both high water salinity and feed utilization efficiency can effectively mitigate CH4 emissions from the coastal shrimp ponds. Overall, the large magnitude of net CH4 emissions observed in our shrimp ponds highlights the urgency of formulating appropriate policies and building sustainable institutions that can strike a balance between land-based aquaculture development and greenhouse gas mitigation in the subtropical coastal regions.