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 Cuxhaven (53.8771 N, 8.7048 E) taken at about 2-7m depth (depending on the tide). The data was obtained between 11 April and 28 August 2021 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 COSYNA Container Cuxhaven. 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. Due to heavy biofouling the external pump of the sensor failed, resulting in data gaps. For a more detailed description see the article cited in References.