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Many seasonally stratified lakes accumulate substantial amounts of the greenhouse gas methane in the anoxic zone. Methane oxidizing bacteria in the water column act as a converter, oxidizing methane into carbon dioxide and biomass before it reaches the atmosphere. Current observations and estimates of this methane oxidation efficiency are diverging, especially for the lake overturn period. Here, we combine a model of turbulent mixing, gas exchange, and microbial growth with a comprehensive data set for autumn mixing to quantify the relevant physical and microbial processes for a 16 m deep, wind‐sheltered Swiss lake. Scenario analysis suggests that the methane converter is efficient and robust under a large range of mixing velocities and only rare events of pronounced surface cooling can trigger substantial outgassing. This case study combines in situ observation and a deterministic physically based model and suggests that the frequency of storms may strongly impact methane emissions for similar temperate lakes. [ABSTRACT FROM AUTHOR]