River estuaries are responsible for high rates of methane emissions to the atmosphere. The complexity and diversity of estuaries require detailed investigation of methane sources and sinks, as well as of their spatial and seasonal variations. The Elbe river estuary and the adjacent North Sea were chosen as the study site for this survey, which was conducted from October 2010 to June 2012. Using gas chromatography and radiotracer techniques, we measured methane concentrations and methane oxidation (MOX) rates along a 60 km long transect from Cuxhaven to Helgoland. Methane distribution was influenced by input from the methane-rich mouth of the Elbe and gradual dilution by methane-depleted sea water. Methane concentrations near the coast were on average 30 ± 13 nmol L−1, while in the open sea, they were 14 ± 6 nmol L−1. Interestingly, the highest methane concentrations were repeatedly detected near Cuxhaven, not in the Elbe River freshwater end-member as previously reported. Though, we did not find clear seasonality we observed temporal methane variations, which depended on temperature and presumably on water discharge from the Elbe River. The highest MOX rates generally coincided with the highest methane concentrations, and varied from 2.6 ± 2.7 near the coast to 0.417 ± 0.529 nmol L−1 d−1 in the open sea. Turnover times varied from 3 to >1000 days. MOX rates were strongly affected by methane concentration, temperature and salinity. We ruled out the supposition that MOX is not an important methane sink in most of the Elbe estuary and adjacent German Bight.