Subtropical lakes are important source of atmospheric methane (CH₄). This study aims to investigate spatial variations of CH₄ flux in Lake Taihu, a large (area 2400 km²) and shallow (mean depth 1.9 m) eutrophic lake in Eastern China. The lake exhibited high spatial variations in pollution level, macrophyte vegetation abundance, and algal growth. We measured the diffusion CH₄ flux via the transfer coefficient method across the whole lake. In addition, data obtained with the flux gradient and the eddy covariance methods were used in conjunction with the data on the diffusion flux to estimate the contribution by ebullition. Results from 3 years' measurements indicated high spatial variabilities in the diffusion CH₄ flux. The spatial pattern of the diffusion CH₄ emission was correlated with water clarity, dissolved oxygen concentration, and the spatial distributions of algal and submerged vegetation. In comparison to the transfer coefficient method, the eddy covariance and the flux gradient method observed a lake CH₄ flux that was 3.39 ± 0.58 (mean ± 1 standard deviation) and 1.95 ± 0.36 times higher in an open‐water eutrophic zone and in a habitat of submerged macrophytes, respectively. The result implied an average of 71% and 49% ebullition contribution to the total CH₄ flux in the two zones. The annual mean diffusion CH₄ flux of the whole lake was 0.54 ± 0.30 g m⁻² yr⁻¹. Our CH₄ emission data suggest that the average CH₄ emission reported previously for lakes in Eastern China was overestimated.

: Nitrous oxide (N₂O) is a potent greenhouse gas and contributes to the loss of stratospheric ozone. However, the role of inland waterbodies in the dynamics of atmospheric N₂O is poorly understood. We investigated N₂O fluxes and their controlling factors in Lake Taihu, a large and shallow (2400 km², 1.9 m depth) eutrophic lake in eastern China. Long‐term measurements (2011–2016) revealed spatial and temporal variations in the lake surface N₂O fluxes. The mean N₂O flux from the lake was 3.5 ± 1.8 (mean ± SD) μmol m⁻² d⁻¹, with an annual N₂O budget of 134.4 ± 69.8 Mg (10⁶ g) yr⁻¹. The highest N₂O fluxes occurred in the eutrophic zone with significant anthropogenic N inputs, and the lowest fluxes occurred in the noneutrophic zone with no external N inflow. A seasonal pattern in N₂O fluxes was observed only in the noneutrophic zone and was strongly correlated with water temperature. No seasonality in the N₂O fluxes was observed in the eutrophic zone with high N concentrations in the water, indicating that N concentrations play a dominant role in regulating N₂O fluxes compared to water temperature. The average N₂O emission factor in Lake Taihu was 0.18%, with temporal and spatial variations negatively associated with N concentration but positively associated with the mass ratio of dissolved organic carbon to dissolved inorganic nitrogen. Our results suggest that anthropogenic activities strongly affect N₂O fluxes in freshwater lakes.