Each year, numerous convective heavy rainfall events cause enormous damage and costs in Austrian municipalities. Due to their complex spatial structures and the increasing degree of imperviousness caused by urbanisation, the risk of flooding in urban catchments is particularly high. Therefore, methods and tools are needed to manage the increasing risk of flooding in urban catchments. The identification of floodplains within a catchment is seen as an essential basis for identifying appropriate measures to reduce the risk of flooding. Integrated 1D-2D models, which take into account hydrological runoff generation on the one hand and surface runoff and sewer discharge on the other hand, are a reliable tool for determining the required target variables—water level and flow velocity—for identifying these flood areas and subsequently analysing the risk. The result is flood risk maps that provide a useful planning tool for municipalities. The methodology presented in this paper describes a step-by-step procedure on how risk maps in urban catchments can be produced by planners and municipalities. The methodology is divided into a preliminary analysis to identify the most critical areas, a detailed analysis to build the integrated 1D-2D model, and a risk analysis to produce the flood risk maps.