Flood mapping is a crucial element of flood risk management. In small and ungauged basins, empirical and regionalization approaches are often adopted to estimate the design hydrographs that represent input data in hydraulic models. In this study, two basins were selected in Slovakia and different methodologies for flood mapping were tested highlighting the role of digital elevation model (DEM) resolution, hydrologic modeling and the hydraulic model. Two DEM resolutions (2 m and 20 m) were adopted. Two hydrologic approaches were employed: a regional formula for peak flow estimation and the EBA4SUB model. Two hydraulic approaches (HEC-RAS and FLO-2D) were selected. Different combinations of hydrologic and hydraulic modeling were tested, under different spatial resolutions. Regarding the DEM resolution, results showed its fundamental importance in the low relief area while its effect was secondary in the moderate relief area. Regarding the hydrologic modeling, results confirmed that it affects the results of the flood areas in the same way independently of DEM resolution and that when using event-based models, the hydrograph shape determination is fundamental. Regarding the hydraulic modeling, this was the step where major differences in the flood area estimation were found.