Increasing water and energy demands, hydroclimatic fluctuations, damming, and usage rights disputes present major challenges in managing transboundary rivers worldwide. Of particular interest is the Eastern Nile River Basin (ENRB), which is subject to broad debate over which modeling approach should be applied to resolve the disparities in transboundary water management among the river’s riparian nations, under increased upstream damming. Several studies have simulated the downstream High Aswan Dam (HAD) storage change during the Grand Ethiopian Renaissance Dam (GERD) filling under different hydrological conditions. However, their findings diverge regarding the impacts of GERD filling on HAD storage, especially when considering a specific, naturalized, historical 10-year period to represent the average flow condition used, as a benchmark for assessing potential downstream impacts. Our extended analysis of the Nile flow historical records demonstrates that considering a single historical 10-year period to simulate the downstream water budget, as performed in Wheeler et al. (Nat Commun 11:5222, 2020, https://doi.org/10.1038/s41467-020-19089-x), widely communicated to policymakers as a robust proof that GERD filling will not generate a deficit at HAD under average flow conditions, is inconclusive as it strongly depend on the selection of the historical inflow period, due to the river high interannual flow variability. Our simulation results of 20 average/near average historical flow periods in Wheeler et al. (Nat Commun 11:5222, 2020, https://doi.org/10.1038/s41467-020-19089-x)’s datasheet indicates that 60% of them generates a downstream water deficit ranging from 0.5 to 14.5 BCM under the same modeling conditions and filling policy. Therefore, considering the simulation results of multiple flow sequences is crucial for accurately reflecting the impact of the Nile’s high interannual flow variability on downstream water deficit assessments, thereby settling the disparities in transboundary water management forecasts for the impacts of GERD filling and operation.