This dataset contains in situ CH4 fluxes measured through the chamber technique over the growing season of 2015 (from July to September) at a wet polygon center and a dry polygon rim in Samoylov Island, Lena River Delta, Northeastern Siberia. A clipping experiment was conducted, resulting in vegetated plots with intact tundra vegetation and clipped and trenched plots where the vegetation was removed. Active layer depths are also presented.