In 2007, the European Floods Directive (FD) 2007/60/EC came into force, introducing a framework for the assessment and management of flood risks. According to Article 6 of the Directive, Member States shall prepare flood hazard maps and flood risk maps at a catchment level, covering the areas that could be flooded under different probability scenarios. The former maps include crucial information towards flood management, such as flood extent-water levels-flow velocity, that will form the base of the flood risk management plans. Based on these data, Member States shall set their objectives and prepare measures concerning their flood management plans. Hence, it is obvious that effective flood management requires reliable methods for the estimation of the flooded areas, such as precise estimation of the peak discharge. This is a hard task for hydrological engineering, taking into account that in the majority of small catchments, especially in Greece, there is a substantial lack of hydrological data. The present paper presents the effect of the uncertainty, derived from lack of data, on the estimation of the peak discharge based upon which the flooded areas will be identified. Towards this direction, a methodology of peak discharge estimation is presented in an ungauged small catchment followed by hydraulic calculations using HEC-RAS and HEC-GeoRAS software packages. The results demonstrate the great variability of the estimated flood extent and the effect of it on the decision-making of the proposed flood measures.