Rivers represent a transition zone between terrestric and aquatic environments, as well as a transition zone between methane rich and methane poor environments. Methane concentrations in freshwater systems are in general higher than in marine systems. The Elbe River is one of the important rivers draining into the North Sea and with the Elbe river high amounts of methane are imported into the water column of the North Sea. The major biological sink is the oxidation of methane by aerobic methanotrophic bacteria. Eight cruises from November 2013 until November 2014 were conducted from Hamburg towards Helgoland. Methane oxidation rate was measured with radiotracers and methanotrophic abundance was assessed by q-PCR. Community fingerprinting was performed with monooxygenase intergenic spacer analysis (MISA). Combining all the data we could identify four environments (marine, coast, outer and inner estuary) with significantly different abundances. The marine environment had lowest abundances and highest abundances were found in the inner estuary. Comparison of the corresponding communities is in progress.