Aquaculture ponds are hotspots of carbon cycling and important anthropogenic sources of the potent greenhouse gas methane (CH₄). Despite the importance of CH₄ ebullition in aquatic ecosystems, its magnitude and spatiotemporal variations in aquaculture ponds remain poorly understood. In this study, we determined the rates and spatiotemporal variations of ebullitive CH₄ emissions from three mariculture ponds during the aquaculture period of two years at a subtropical estuary in southeast China. Our results showed that the mean ebullitive CH₄ flux from the studied ponds was 14.9 mg CH₄ m⁻² h⁻¹ during the aquaculture period and accounted for over 90% of the total CH₄ emission, indicating the importance of ebullition as a major CH₄ transport mechanism. Ebullitive CH₄ emission demonstrated a clear seasonal pattern, with a peak value during the middle stage of aquaculture. Sediment temperature was found to be an important factor influencing the seasonal variations in CH₄ ebullition. Ebullitive CH₄ fluxes also exhibited considerable spatial variations within the ponds, with 49.7–71.8% of the whole pond CH₄ ebullition being detected in the feeding zone where the large loading of sediment organic matter fueled CH₄ production. Aquaculture ponds have much higher ebullitive CH₄ effluxes than other aquatic ecosystems, which indicated the urgency to mitigate CH₄ emission from aquaculture activities. Our findings highlighted that the importance of considering the large spatiotemporal variations in ebullitive CH₄ flux in improving the accuracy of large-scale estimation of CH₄ fluxes in aquatic ecosystems. Future studies should be conducted to characterize CH₄ ebullitive fluxes over a greater number and diversity of aquaculture ponds and examine the mechanisms controlling CH₄ ebullition in aquatic ecosystems.