In recent decades, natural hazards have caused major disasters in the natural and man-made environment. Floods are one of the most devasting natural hazards with high mortality percentage, destruction of infrastructure and large financial losses. This study presents a methodological approach for flood risk management at lakes and adjacent areas that is based on the implementation of the EU Floods Directive (2007/60/EC) in Greece. Contemporary engineering approaches have been used for the estimation of the inflow hydrographs. The hydraulic-hydrodynamic simulations implemented in the following order: a) hydrologic modelling of lake tributaries and estimation flood flow inflow to the lake, b) flood inundation modelling of lake tributaries, c) simulation of the lake as a closed system, d) simulation of the lake outflows to the adjacent areas, e) simulation of flood inundation of rural and urban areas adjacent to the lake. The hydrologic modelling has been performed using the HEC-HMS model and the hydraulic-hydrodynamic simulations were implemented with the use of the two-dimensional HEC-RAS model. The simulations applied for three soil moisture conditions (dry, medium and wet) and three return periods (T = 50, T = 100 and T = 1000 years) and a methodology was followed for the flood inundation modelling in urban areas. Upper and lower estimates on water depths, flow velocities and inundation areas are estimated for all inflow hydrographs and for varying roughness coefficient values. The proposed methodology presents the necessary steps and the results for the assessment of flood risk management and mapping for lake and adjacent urban and rural areas. The methodology has been applied to Pamvotida lake, Epirus, Greece, which is the lake of Ioannina city.