The construction of large-scale water reservoir facilities in transboundary river basins always arouses intense concern and controversy. The Grand Ethiopian Renaissance Dam (GERD) under construction in Ethiopia is perceived to affect water security in Egypt and Sudan. Therefore, this study investigated the water and sediment balance of the Blue Nile River (BNR) basin and identified the spatio-temporal variation in sediment and water yields along with the construction of GERD using Integrated Valuation of Ecosystem Services and Tradeoffs (InVEST) sediment and water yield models. The BNR basin experienced increasing water and sediment yields between 1992 and 2020 and has shown a growth trend since 2020. The lion’s share of water and sediment yields come from upstream of the GERD. Taken together, these results imply that the construction of the GERD will serve as a water storage and silt trap for Sudan and Egypt.