The data set contains methane (CH4) ebullition and diffusion fluxes from three locations at Lake Neusiedl in Austria, measured weekly from late March to mid-July 2021: Channel (CH), Reed belt (RB), and Open water/Lake (OW). Fluxes are expressed daily. Stable carbon isotopes of the ebullition gas were determined with a Picarro G2201-i. The following in-situ water measurements were carried out during the same period and reported here: water temperature (Twater), water level (WL), dissolved oxygen (DO), pH, electric conductivity (EC), oxidation/reduction potential (ORP). Finally, water samples were also collected weekly, at the same sites. From those samples, the following parameters were analyzed in the lab and reported here: Nitrate (NO3_-), nitrite (NO2_-), ammonium (NH4_+), orthophosphate (PO4_3-), sulfate (SO4_2-), total dissolved nitrogen (TDN), dissolved inorganic carbon (DIC), dissolved non-purgeable organic carbon (NPOC). File format: CSV The data set corresponding to the publication: Baur, P.A.; Henry Pinilla, D.; Glatzel, S. (2024): Is ebullition or diffusion more important as methane emission pathway in a shallow subsaline lake? Science of the Total Environment. 912, 169112. https://doi.org/10.1016/j.scitotenv.2023.169112