The Lena River is one of the largest Russian rivers draining into the Laptev Sea. The permafrost areas surrounding the Lena are predicted to thaw at increasing rates due to global temperature increases. With this thawing, large amounts of carbon – either organic or in the gaseous forms carbon dioxide and methane – will reach the waters of the Lena and the adjacent Buor-Khaya Bay (Laptev Sea). Methane concentrations and the isotopic signal of methane in the waters of the Lena Delta and estuary were monitored from 2008 to 2010. Creeks draining from permafrost soils produced hotspots for methane input into the river system (median concentration 1500 nM) compared with concentrations of 30–85 nM observed in the main channels of the Lena. No microbial methane oxidation could be detected; thus diffusion is the main process of methane removal. We estimated that the riverine diffusive methane flux is 3–10 times higher than the flux from surrounding terrestrial environment. To maintain the observed methane concentrations in the river, additional methane sources are necessary. The methane-rich creeks could be responsible for this input. <br><br> In the estuary of Buor-Khaya Bay, methane concentrations decreased to 26–33 nM. However, within the bay no consistent temporal and spatial pattern could be observed. The methane-rich waters of the river were not diluted with marine water because of a strong stratification of the water column. Thus, methane is released from the estuary and from the river mainly by diffusion into the atmosphere.