To compare the carbon fluxes between semi-terrestrial tundra and ponds, which cover a significant fraction of northern peatlands, we installed a temporary Eddy Covariance tower next to a merged polygonal pond in the Lena River Delta. The resulting dataset includes the sensible heat flux, latent heat flux, CO2 flux, and CH4 flux. Additionally, the dataset contains meteorological observations, an estimate of the footprint coverage, and estimated CO2 fluxes from the merged polygonal pond and the semi-terrestrial polygonal tundra, respectively. The dataset was recorded between 11 July and 10 September 2019. Further information on the dataset can be found in https://doi.org/10.5194/bg-19-1225-2022