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The availability of lake bathymetry maps is imperative for estimating lake water volumes and their variability, which is a sensitive indicator of climate. It is difficult, if not impossible, to obtain bathymetric measurements from all of the thousands of lakes across the globe due to costly labor and/or harsh topographic regions. In this study, we develop a new digital lake bathymetry model (DLBM) using the step-wise water recession method (WRM) to generate 3-dimensional lake bathymetric maps based on the digital elevation model (DEM) alone, with two assumptions: (1) typically, the lake’s bathymetry is formed and shaped by geological processes similar to those that shaped the surrounding landmasses, and (2) the agent rate of water (the thickness of the sedimentary deposit proportional to the lake water depth) is uniform. Lake Ontario and Lake Namco are used as examples to demonstrate the development, calibration, and refinement of the model. Compared to some other methods, the estimated 3D bathymetric maps using the proposed DLBM could overcome the discontinuity problem to adopt the complex topography of lake boundaries. This study provides a mathematically robust yet cost-effective approach for estimating lake volumes and their changes in regions lacking field measurements of bathymetry, for example, the remote Tibetan Plateau, which contains thousands of lakes.