Analysing the hydrological vulnerability of important structures such as bridges is essential to ensuring people’s safety. This research proposes a methodology to assess the hydrological vulnerability of riverine bridges through a case study of the Bajo Grau Bridge in the city of Arequipa, Peru. Topological and hydrometrical data collection play an important role in the study. A topographic surveying of the bridge and the streambed were carried out, followed by a series of annual maximum flow rates which were compiled, fitted with empirical and theoretical distribution functions, and used in a probability analysis. Based on this process, the flow rates were estimated for six scenarios based on different return periods and critical conditions. Once the hydrological study was completed, the system was modelled using HEC-RAS. The hydraulic simulation, as well as the soil mechanics study, provided the parameters to calculate the scour in the bridge substructure, the potential erosion in the deck, and the possibility of flooding in the superstructure. A hydrological vulnerability assessment matrix with ten criteria subdivided in environmental and physical vulnerabilities was designed and used to determine that the bridge has a high hydrological vulnerability. The proposed methodology can be adapted and transferred to assess other bridges with similar characteristics.