The dataset is about temporal variability of dissolved methane along the freshwater-sea continuum in northern Germany. Sensors were installed at fixed stations at in total three sites at different water depths. This dataset is from the station in Heligoland (54.1833 N, 7.8667 E) at about 9-12m depth (depending on the tide). The data was obtained between 27 April and 28 October in high frequency measurements (1 min) with a methane sensor from Kongsberg (4H Jena model CONTROS HydroC CH4,). Methane concentrations were calculated according to manufacturer's instructions, based on temperature and salinity values from UW-node Heligoland (Fischer, Philipp; Happel, Lea; Brand, Markus; Eickelmann, Laura; Lienkämper, Miriam; Bussmann, Ingeborg; Anselm, Norbert; Brix, Holger (2022): Hydrographical time series data of Helgoland, Southern North Sea, 2021. PANGAEA, https://doi.org/10.1594/PANGAEA.950173). A gap in the salinity data was replaced with the median value of the observed time span (31.66). For the quality control of the data a local range of 0.1 – 1000 nmol/L was set, a technical range for the pump power 2 – 8. Watt, a spike and gradient value of 1. For a more detailed description see the article cited in References.