In recent years, new advances in remote sensing techniques have made Digital Elevation Models (DEMs) become popular elevation data sources for delineating catchment boundaries. This application of DEMs is particularly useful in water accounting and river basin management for Vietnam, of which the river network has very high drainage density and has been facing many pressures arising from recent economic advances. However, catchment delineated from DEMs is highly dependable to the quality of original data sources, leading to potential discrepancy in the shape as well as catchment area of the boundaries delineated from different DEMs over specific locations in Vietnam. This study comprehensively investigates this issue by analyzing the differences across catchment boundaries delineated from the most popular DEMs (i.e., HydroSHEDS, MERIT, and TanDEM–X). The impacts of these discrepancies (due to using different DEMs) on identifying areal rainfall from a gridded data product are assessed to highlight the importance of selecting DEM data sources that are suitable for specific study area.