AbstractLakes in the Alpine region are recognized as critical methane (CH₄) emitters, but a robust characterization of the magnitude and variability of CH₄ fluxes is missing. We developed a mobile platform for CH₄ eddy covariance (EC) flux measurements to tackle this gap. The mobile system was deployed at nine lakes across a latitudinal transect in the Alps and validated by comparing the measured fluxes with fixed on‐shore EC station and to chamber and boundary layer flux estimates. Our approach was shown to be well suited to capture different CH₄ emission pathways and to integrate the within lake variability, therefore, overcoming the limitations of other methods (e.g., boundary layer method). Additionally, this mobile system offers a tool to characterize inter‐lake variability of fluxes with consistent measurements. Methane fluxes were explained by dissolved nitrogen, total phosphorus, dissolved oxygen, seston and lake size. The highest fluxes and most substantial seasonal variability were found in a shallow low‐altitude lake in the Southern Alps. We suggest that characterizing the intra‐lake emission heterogeneity and consistent measurements for a better understanding of inter‐lake emission differences is fundamental for a solid estimate of freshwater CH₄ budgets.