This dataset contains outline polygons and water area time series of supraglacial lakes at the two main glacier systems of the Northeast Greenland Ice Stream, Nioghalvfjerdsbræ (also known as 79°N Glacier) and Zachariæ Isstrøm. The dataset was derived from Polarimetric Synthetic Aperture Radar observations (PolSAR) of the ESA satellites Sentinel-1A and Sentinel-1B during 2017-2020 and consists of a polygon file defining the lake outline definitions, a NetCDF file containing time series of water area and further parameters for each lake and a PDF with further details to the other files content. It was created as part of the European Union's Horizon 2020 research and innovation programme via project iCUPE (Integrative and Comprehensive Understanding on Polar Environments).