Environmental controls on methane (CH) emission from lakes are poorly understood at sub-daily time scales due to a lack of continuous data, especially for ebullition. We used a novel technique to partition eddy covariance CH flux observed in the littoral zone of a mid-latitude shallow lake in Japan and examined the environmental controls on diffusion and ebullitive CH flux separately at a sub-daily time scale during different seasons. Both diffusive and ebullitive flux were significantly higher in summer than winter. The contribution of ebullitive flux to total flux was 56% on average. Diffusive flux increased with increasing wind speed due to increased subsurface turbulence. For a given wind speed, diffusive flux was higher in summer than in winter due to the higher concentration of dissolved CH in the surface water during summer. The transfer of accumulated dissolved CH from the bottom layer to the surface in summer and the accumulation of dissolved CH under surface ice in winter were important for explaining the variability of diffusive flux. In summer, ebullition tended to occur following triggers such as a decrease in hydrostatic pressure or an increase in wind speed. In winter, on the other hand, the impact of triggers was not obvious, and ebullition tended to occur in the morning when the wind speed began to increase. The low CH production rate in winter slowed the replenishment of bubbles in the sediment, negating the effect of triggers on ebullition.