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Large greenhouse gas emissions occur via the release of carbon dioxide (CO2) and methane (CH4) from the surface layer of lakes. Such emissions are modeled from the air-water gas concentration gradient and the gas transfer velocity (k). The links between k and the physical properties of the gas and water have led to the development of methods to convert k between gases through Schmidt number normalization. However, recent observations have found that such normalization of apparent k estimates from field measurements can yield different results for CH4 and CO2. We estimated k for CO2 and CH4 from measurements of concentration gradients and fluxes in four contrasting lakes and found consistently higher (on an average 1.7 times) normalized apparent k values for CO2 than CH4. From these results, we infer that several gas-specific factors, including chemical and biological processes within the water surface microlayer, can influence apparent k estimates. We highlight the importance of accurately measuring relevant air-water gas concentration gradients and considering gas-specific processes when estimating k.