Although freshwaters are considered to be substantial natural sources of atmospheric methane (CH₄), in situ processes of CH₄ production and consumption in freshwater ecosystems are poorly understood, especially in subtropical area. To improve our understanding of CH₄ dynamics in subtropical lakes, we examined vertical and seasonal profiles of dissolved CH₄ and its carbon isotope ratio (d¹³C) in the deep subtropical Fei-Tsui Reservoir (Taiwan), whose winter vertical mixing varies with the climatic condition. In years with an incomplete vertical mixing and the subsequent strong thermal stratification, resulting in profundal hypoxia, we found increases in sedimentary CH₄ production and storage. In contrast, in years with a strong winter vertical mixing to the bottom of the reservoir, CH₄ production was suppressed. Diffusive emissions from profundal CH₄ storage seemed to be negligible due to the efficiency of CH₄ oxidation during ascent through the methane oxidizing bacteria (MOB) activity. Most of the profundal CH₄ was rapidly oxidized by MOB in both oxic and anoxic layer, as characterized by its carbon isotope signature, whereas aerobic CH₄ production in a subsurface layer, which may be enhanced under high temperature in summer, may account for a large portion of atmospheric CH₄ emissions from this reservoir.