Extreme precipitation and flooding events are rising globally, necessitating a thorough understanding and sustainable management of water resources. One such setting is the Nile River's source areas, where high precipitation has led to the filling of Lake Nasser (LN) twice (1998-2003; 2019-2022) in the last two decades and the diversion of overflow to depressions west of the Nile, where it is lost mainly to evaporation. Using temporal satellite-based data, climate models, and continuous rainfall-runoff models, we identified the primary contributor to increased runoff that reached LN in the past two decades and assessed the impact of climate change on the LN's runoff throughout the twenty-first century. Findings include: (1) the Blue Nile subbasin (BNS) is the primary contributor to increased downstream runoff, (2) the BNS runoff was simulated in the twenty-first century using a calibrated (1965-1992) rainfall-runoff model with global circulation models (GCMs), CCSM4, HadGEM3, and GFDL-CM4.0, projections as model inputs, (3) the extreme value analysis for projected runoff driven by GCMs' output indicates extreme floods are more severe in the twenty-first century, (4) one adaptation for the projected twenty-first century increase in precipitation (25-39%) and flood (2%-20%) extremes is to recharge Egypt's fossil aquifers during high flood years.