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The Grand Ethiopian Renaissance Dam (GERD) filling and operation is a highly sensitive issue for Egypt and Sudan. A recently accepted manuscript by Heggy et al (2021 Environ. Res. Lett. 16 074022) assessed the water deficit for Egypt based on different scenarios for the first filling of GERD lake and estimated 31 billion cubic meters per year under a 3 year filling scenario. We would like to present grossly mischaracterized assumptions, inaccurate data, and controversial conclusions found in this accepted manuscript through this rebuttal. Although the accepted manuscript does not include any new analysis of the River Nile Hydrology, the results of previous substantive studies were misinterpreted or ignored. Moreover, we have serious concerns about the basic hydrological assumptions that are the basis for the economic impacts and the potential loss of the Egyptian agricultural lands. The main methodological flaws of concerns are (a) how the deficit is calculated, losses from GERD, especially the evaporation losses that contradicts several previous studies (e.g. Wheeler et al 2016 Water Int. 41 611–34; Eldardiry and Hossain 2020 J. Hydrol. 125708; Wheeler et al 2020 Nat. Commun. 11 1–9); (b) neglecting the normal role of High Aswan Dam (HAD) reservoir and directly linking the deficit of the water budget to an immediate loss of agricultural lands with all other associated exaggerated economic impacts estimates; (c) including highly exaggerated seepage losses from the GERD lake; (d) neglecting the updated situation of Aswan High Dam reservoir levels and the GERD’s infrastructure itself, and (e) quantifying the impacts of potential changes of water level on HAD reservoir on the Nubian aquifer. We herein present a direct fact-checking approach including the studies cited in the accepted manuscript. We believe that this critical comment paper can serve as a basis for defending scientific integrity and contributes to cooperation and peace in the region.