The geological environment is undoubtedly one of the basic factors that influence the formation of surface runoff. The extent to which this factor can also affect the hydrodynamic characteristics of flash floods, which is also indirectly associated with flood risk, is the main topic of this study. In two geologically different areas of the Bohemian Massif (crystalline rocks predominate) and the western Carpathians (flysch rocks predominate), a total of 40 watersheds characterised by sharing a certain hydrological analogy were selected (20 watersheds from the Massif and 20 from the Flysch zone). In each of these watersheds, 1-year, 10-year and 100-year flash flood return periods were constructed using the two-dimensional hydrodynamic model Iber. The outputs from this model included raster datasets of areas, depths, and flow velocities during inundations. Subsequently, these rasters were analysed and compared with an emphasis on differences within the individual geological study areas. The outputs showed clear differences in the individual hydrodynamic characteristics (e.g. the average inundation area during Q100 was 29.07% larger in the Flysch than in the Massif). Overall, the Flysch zone appeared to be far riskier in terms of flash floods than in the case of the Bohemian Massif.