Large methane emission from freshwater aquaculture ponds revealed by long-term eddy covariance observation

•Methane fluxes from freshwater aquaculture ponds were measured using eddy covariance.•Ebullition was the main transport way accounting for 70%±4% of the total CH4 flux.•Water temperature was the primary driver of the CH4 flux across multiple time scales.•Large spatial variations were observed in the total and ebullitive CH4 flux with the FC and IF method.•Dredging plays a more important role in regulating the CH4 emission than aeration.