Rivers represent a transition zone between terrestrial and aquatic environments, as well as a transition zone between methane rich and methane poor environments. Methane concentrations are generally higher in freshwater systems than in marine systems. The Elbe River is one of the crucial drainages into the North Sea and by this high amounts of methane are imported into the marine water column. Oxidation of methane by aerobic methanotrophic bacteria is the major biological sink. Six cruises from November 2013 until June 2014 were conducted along the salinity gradient from Hamburg towards Helgoland. Methane oxidation rate was measured with radiotracers and the abundance of methanotrophic bacteria was assessed via real-time PCR. A newly designed primer targeting the genomic sequence encoding the α-subunit of the functional pMMO enzyme in water column organisms was amplified and tested against the conventional primer set. At the marine stations the cell number was relatively stable with 3 x 104 cells per L, while in the Elbe cell numbers ranged between 103 – 106 cells per L. Environmental parameters (temperature, salinity, SPM) seemed to have no influence on the abundance. However the interaction between activity and abundance seemed to be more complex.