The dataset comprises data collected from nine specifically chosen lakes located across the eastern Alps during the ALCH4 project. The primary objective of this project was to assess the efficacy of a mobile Eddy Covariance platform in characterizing CH4 emissions. The field measurements were conducted throughout the ice-free periods in the years 2018 and 2019. This dataset encompasses: i) the EddyPro 7.0.6 (LI-COR Inc., Lincoln, NE, USA) output for all Eddy Covariance campaigns; ii) outcomes of the chamber measurements; iii) data obtained from surface samples. This research was funded by the Autonomous Province of Bozen/Bolzano.