The Lena River is one of the biggest Russian rivers draining into the Laptev Sea. Due to predicted increasing temperatures, the permafrost areas surrounding the Lena Delta will melt at increasing rates. With this melting, high amounts of methane will reach the waters of the Lena and the adjacent Laptev Sea. Methane oxidation by methanotrophic bacteria is the only biological way to reduce methane concentrations within the system. However, the polar estuary of the Lena River is a challenging environment for bacteria, with strong fluctuations in salinity and temperature. We determined the activity (tracer method) and the abundance (qPCR) of aerobic methanotrophic bacteria. We described the methanotrophic population with MISA; as well as the methane distribution (head space) and other abiotic parameters in the Lena Delta in September 2013. In riverine water (S 〈 5) we found a median methane concentration of 22 nM, in mixed water (5 〈 S 〈 20) the median methane concentration was 19 nM and in polar water (S 〉 20) a median 28 nM was observed. The Lena River was not the methane source for surface water, and bottom water methane concentrations were mainly influenced by the concentration in surface sediments. However, the methane oxidation rate in riverine and polar water was very similar (0.419 and 0.400 nM/d), but with a higher relative abundance of methanotrophs and a higher estimated diversity with respect to MISA OTUs in the rivine water as compared to polar water. The turnover times of methane ranged from 167 d in mixed water, 91 d in riverine water and only 36 d in polarwater. Also the environmental parameters influencing the methane oxidation rate and the methanotrophic population differed between the water masses. Thus we postulate a riverine methanotrophic population limited by sub-optimal temperatures and substrate concentrations and a polar methanotrophic population being well adapted to the cold and methane poor environment, but limited by the nitrogen content. The diffusive methane flux into the atmosphere ranged from 4–163 µmol m2 d−1 (median 24). For the total methane inventory of the investigated area, the diffusive methane flux was responsible for 8 % loss, compared to only 1 % of the methane consumed by the methanotrophic bacteria within the system.