Lakes have a controversial climate footprint. In fact, they are a sink of CO2 but at the same time they can be an important source of CH4. Indeed, a global synthesis of methane emission data (Bastviken et al., 2011) suggests that freshwater ecosystems - in particular lakes - may be much larger sources of methane than previously thought, questioning current methane budgets and the general role of freshwater ecosystems in the greenhouse gas balance. The main objective of this study is to improve data availability and quality regarding methane emissions from lakes in the Alpine region - a region that presently is heavily under-represented in global data sets - in order to allow a robust assessment of their role in the global greenhouse gas balance. This is of fundamental importance for the assessment of CH4 emissions from regions particularly sensitive to an increasing climatic variability. Aiming at spatial and temporal representativeness of flux measurements, we made use of an innovative mobile eddy covariance system. We installed the instruments on a small boat, and we performed measurements while cruising. Meteorological and bio-physical data got recorded simultaneously to investigate drivers of gas fluxes by means of empirical modelling. Additionally, we made use of classical chamber measurements for validating our approach. In this fashion, we investigated a number of natural and man-made lakes across a transect of two degrees of latitude across the Alps. In fact, the alpine region provides a unique opportunity to assess the role of environmental drivers on GHG emissions over a limited latitudinal range in an altitude-for-time substitution manner. We repeatedly visited target lakes across the ice-free season during the years 2018 and 2019. We demonstrated that our method is valid for capturing methane emissions from different pathways (diffusion but also ebullition and transport through vegetation). We found that most of the lakes are supersaturated and the highest emissions were measured in shallow and eutrophic lakes at low altitude. In conclusion, with this study we were able to develop new insights on the role of freshwater ecosystems in the global methane budget. References: Bastviken D, Tranvik LJ, Downing JA, Crill PM, Enrich‐Prast A (2011). Freshwater methane emissions offset the continental carbon sink. Science 331, 50.