The River Elbe, as one of the major waterways of central Europe, is a potential source of high amounts of methane into the North Sea. Twelve sampling cruises from October 2010 until June 2013 were conducted from Hamburg towards the mouth of the Elbe at Cuxhaven. The dynamic of methane concentrations in the water column and its consumption via methane oxidizing bacteria was measured. In addition, physico-chemical parameters were used to estimate their influence on the methanotrophic activity. We observed high methane concentrations at the stations in the area of Hamburg harbour (“upper estuary”) and about 10 times lower concentrations in the lower estuary (median of 416 versus 40 nmol L−1, respectively). The methane oxidation rate mirrored the methane distribution with high values in the upper estuary and low values in the lower estuary (median of 161 versus 10 nmol L−1 day−1, respectively). Methane concentrations were significantly influenced by the river hydrology (falling water level) and the biological oxygen demand while interestingly, no clear relation to the amount of suspended particulate matter (SPM) was found. Methane oxidation rates were significantly influenced by methane concentration and to a lesser extent by temperature. Methane oxidation accounted for 41 ± 12 % of the total loss of methane in summer/fall periods, but for only 5 ± 3 % of the total loss in the winter/spring periods (total loss = methane oxidation + diffusion into the atmosphere). The average sea-air flux of methane was 33 ± 8 g CH4 m−2 y−1. We applied a box model taking into account the residence times of each water parcel depending on discharge and tidal impact. We observed almost stable methane concentrations in the lower estuary, despite a strong loss of methane through diffusion and oxidation. Thus we postulate that losses in the lower Elbe estuary were balanced by additional inputs of methane, possibly from extensive salt marshes near the river mouth.