Manual water diversion has been applied to improve the water environment of lake, however, its effects on CH₄ diffusion flux across water-air interface have not been well documented. To improve the water quality of Lake Taihu, the project of water transfers from Yangtze River is a long-term effort. As the first stop that water transfers into Lake Taihu from Yangtze River, Gonghu Bay is the fine place to evaluate the effects of water diversion on lake CH₄ flux. Field measurements from November 2011 to August 2013 showed that, the CH₄ diffusion flux at Gonghu Bay with a mean value of 0.073 mmol/(m²·d) was significantly higher than at the central zone with a mean value of 0.017 mmol/(m²·d). Meanwhile, CH₄ flux varied among sites at Gonghu Bay. The CH₄ flux at the two-zone both showed temporal variability, which was regulated by water temperature. However, the role of temperature varied among the two zones, the water diversion may confound the effect of temperature on CH₄ flux at Gonghu Bay, leading to the relatively less temperature dependency of CH₄ flux. Manual water diversion increased the lake CH₄ emission flux as a whole, however, lake CH₄ emission was controlled by multiple, interconnected factors related to internal metabolic activities and external loading, further studies are needed to explore the underlying mechanism.