Estuaries are complex systems, which are expected to hold a big share of global oceanic methane emissions to the atmosphere. Rivers are considered to be the main contributors of methane for coastal seas, whereas both the role and impact of tidal flats are still unclear. The river Elbe being one of the major waterways in central Europe, makes the selected site in the southern North Sea a highly relevant case study. In the conducted research the role of the Elbe Estuary as a source of methane in the North Sea was investigated and the effect of environmental parameters on the methane distribution was explored. With high spatial and temporal resolution, the methane distribution in surface waters was obtained in autumn 2018 with a new system comprising of a degassing unit followed by analysis with off-axis integrated cavity output spectroscopy. Shipborne analysis and measurements at a fixed station were performed. For the measurements close to the shore, a dilution process of methane enriched riverine water and lateral input from tidal flats with methane depleted seawater was observed, affected by a strong tidal influence. The water showed a tidally impacted methane pattern with maximum concentrations up to 5 times higher during low tide than concentrations during high tide. The Elbe Estuary was shown to be a source of methane to the atmosphere. Future studies should consider tidal variations to reduce uncertainties of dissolved methane measurements and methane flux estimations of estuarine systems, hence improve the global methane budget calculations. The role of estuaries as methane sources and their influence on the climate highlight the importance of eradicating these uncertainties.