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We studied the concentrations and diffusive fluxes of carbon dioxide (CO₂) and methane (CH₄) in 12 lakes in a size range of 0.004–35 km² and mean total organic carbon (TOC) range of 6–25 mg L⁻¹, located in the southern boreal area of Finland. TOC, mainly originating from the catchment, was the best predictor of concentrations and areal CO₂ effluxes in the whole lake‐area range, but among the lakes with an area < 1 km² having an anoxic hypolimnion during summer, the areal effluxes were also related to lake size and an index of turbulence. The concentration and areal effluxes of CH₄ from the lakes' pelagic zones were related more closely to lake‐size‐related water column stability and turbulent mixing than directly to TOC. The total regional flux estimate from 619 lakes in the region of 1600 km² showed that seven lakes with an area of 10–50 km² were responsible for 57–69% of the pelagic CO₂ effluxes …