Enclosure lake aquaculture causes lake eutrophication and emits CH4 to the atmosphere. So far, little is known about the rate of CH4 emission from lake aquaculture and about how ecological restoration (or aquaculture abandonment) affects the emission. In this study, the eddy covariance (EC) technique was deployed to quantify the CH4 flux in an enclosure lake aquaculture farm and to investigate the flux response to ecological restoration. The lake site under aquaculture farming emitted 36.0 g C-CH4 m(-2) yr(-1) to the atmosphere, an amount that is comparable to the global mean value of semi-intensive aquaculture systems. The annual CH4 emission decreased from the pre-restoration level by 34% and 37% to 23.7 and 22.8 g C-CH4 m(-2) yr(-1) in the first and second year of ecological restoration, respectively, but was still much higher than that at a reference lake site not impacted by aquaculture farming (6.12 g C-CH4 m(-2) yr(-1)). The high emission values after aquaculture abandonment suggest that aquafeed input in the decades of farming may have caused accumulation of a large amount of organic carbon in the sediment that continues to fuel CH4 production and that it may take a long time for the system to recover to a natural state. After aquaculture abandonment, floating-leaved plants expanded rapidly within the EC flux footprint, resulting in a high net ecosystem productivity (NEP) in the growing season. These plants appeared to be able to transport CH4 to the atmosphere through aerenchyma tissues and stomata.