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Shallow thermokarst lakes are important sources of greenhouse gases (GHGs) such as methane (CH4) and carbon dioxide (CO2) resulting from continuous permafrost thawing due to global warming. Concentrations of GHGs dissolved in water typically increase with decreasing lake size due to coastal abrasion and organic matter delivery. We hypothesized that (i) CH4 oxidation depends on the natural oxygenation gradient in the lake water and sediments and increases with lake size because of stronger wind‐induced water mixing; (ii) CO2 production increases with decreasing lake size, following the dissolved organic matter gradient; and (iii) both processes are more intensive in the upper than deeper sediments due to the in situ gradients of oxygen (O2) and bioavailable carbon. We estimated aerobic CH4 oxidation potentials and CO2 production based on the injection of 13C‐labeled CH4 in the 0–10 cm and 10–20 cm sediment depths of small (~300 m2), medium (~3000 m2), and large (~106 m2) shallow thermokarst lakes in the West Siberian Lowland. The CO2 production was 1.4–3.5 times stronger in the upper sediments than in the 10–20 cm depth and increased from large (158 ± 18 nmol CO2 g−1 sediment d.w. h−1) to medium and small (192 ± 17 nmol CO2 g−1 h−1) lakes. Methane oxidation in the upper sediments was similar in all lakes, while at depth, large lakes had 14‐ and 74‐fold faster oxidation rates (5.1 ± 0.5 nmol CH4‐derived CO2 g−1 h−1) than small and medium lakes, respectively. This was attributed to the higher O2 concentration in large lakes due to the more intense wind‐induced water turbulence and mixing than in smaller lakes. From a global perspective, the CH4 oxidation potential confirms the key role of thermokarst lakes as an important hotspot for GHG emissions, which increase with the decreasing lake size. [ABSTRACT FROM AUTHOR]