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• Two-way coupling improved the simulation and projection for lake evaporation. • All NBS components are projected to increase in the future. • Water levels in the Great Lakes are projected to rise in the future. The Great Lakes of North America are the largest unfrozen surface freshwater system in the world and many ecosystems, industries, and coastal processes are sensitive to the changes in their water levels. The water levels of the Great Lakes are primarily governed by the net basin supplies (NBS) of each lake which are the sum of over-lake precipitation and basin runoff minus lake evaporation. Recent studies projected the future NBS of the Great Lakes by dynamically downscaling General Circulation Models (GCMs) using Regional Climate Models (RCMs). However, their RCMs had been coupled to one-dimensional (1D) lake column models which lack the ability to accurately simulate the Great Lakes' hydrodynamics and thermal structure. In this study, an ensemble of three dynamical downscalings based on the Great Lakes-Atmosphere Regional Model (GLARM) is used to project the future NBS and water level of the Great Lakes. GLARM is a three-dimensional (3D) regional climate modeling system for the Great Lakes region that two-way couples an RCM to a 3D hydrodynamic lake and ice model, making this the first study to use such an advanced model for water level projection of the Great Lakes. For the present-day climate, over-lake precipitation and lake evaporation simulated by GLARM, along with the basin runoff simulated by the GLARM-driven Large Basin Runoff Model (LBRM), track the mean seasonal cycle of the NBS components remarkably well. In particular, compared to previous studies, the most significant improvements are made in estimating the lake evaporation. For future hydroclimate, the ensemble average projects an increase in annual NBS and average annual water level for each lake. The projected NBS increase is mostly due to an increase in over-lake precipitation and basin runoff combined with a relatively smaller increase in lake evaporation. According to the ensemble average, by 2040–2049, the average annual water levels of Lake Superior, Michigan-Huron, and Erie are projected to increase by +0.19, +0.44, and +0.28 m, respectively, relative to 2010–2019. The individual downscaling cases highlight the uncertainty in climate projection, showing both increases and decreases in annual NBS and water level projection. The projected changes in the average annual water levels by 2040–2049 relative to 2010–2019 range from −0.01 to +0.32 m in Lake Superior, −0.13 to +0.80 m in Lake Michigan-Huron and −0.09 to +0.54 m in Lake Erie. [ABSTRACT FROM AUTHOR]