Aquaculture ponds are important anthropogenic methane (CH₄) sources to the atmosphere. Currently large uncertainties still remain regarding the emission strength of this source type and its relationship with aquacultural farming practices. In this study, the methane flux was measured continuously for four years with eddy covariance (EC) in an aquaculture pond complex in the Yangtze River Delta, China. These ponds have never been dredged and were aerated during part of the aquacultural season. Additionally, floating chambers and inverted funnels were used to investigate spatial heterogeneity of the CH₄ flux and to quantify the contribution via ebullition to the flux. The results showed that the daily CH₄ flux ranged from 0.1 to 16.7 μg m⁻² s⁻¹, with an average value of 4.10 ± 3.08 µg m⁻² s⁻¹. Water temperature was the primary driver of the CH₄ flux across multiple time scales (half-hourly, daily, and monthly scale). Ebullition was the main transport way accounting for 70% ± 4% of the total CH₄ flux. The annual flux in this study was about three times the median flux reported by other researchers for similar freshwater aquaculture ponds. A statistical analysis of our data together with the published flux data reveals that ponds with dredging have much lower CH₄ emission flux than those without dredging and suggests that dredging may have a much larger influence on the emission flux than aeration.