In addition to their ecological importance, rivers and streams have always been used in diverse ways by humans, resulting in the development of settlements and their connected built environments along many of the world's watercourses. During heavy rainfall, buildings, traffic infrastructure and water‐related infrastructure are exposed to potential hazards in the form of (flash) floods. In contrast to near‐natural watercourses, anthropogenically modified channels in urban areas are particularly susceptible to damage by flooding. Previous damage assessments have highlighted the need to forecast such damage to watercourses in order to identify critical areas and justify the selection and expansion of adaptation measures. Within the scope of the current study, we have developed a method based on the hydro‐morphological properties of watercourses to make transferable estimates of the economic damage potential based on ecologically‐relevant parameters. Using a scale‐specific cause‐effect analysis, we have identified characteristics of the watercourse type and adjacent structures as well as construction‐related properties of reinforcements that can increase the damage potential during flooding. In this way, we are able to show that several influencing factors determine the vulnerability of watercourses: in addition to the specific longitudinal gradient and size (macroscale) of various watercourse types, damage‐relevant boundary conditions in watercourse sections (mesoscale) and the resistance of typical bed and bank constructions are also important, reflecting the specific structural conditions. Taking rivers in Germany and the Czech Republic as case studies, in the following, we review the local identification of critical areas and describe the necessary data management. The presented “Hydro‐morphological based Vulnerability Assessment‐Concept (HyVAC)” can contribute to the flood damage prevention at watercourses by utilizing existing basic data to the greatest possible extent and thus is suitable for preliminary investigations according to the EC Flood Risk Management Directive.