•Three-step risk-based methodology for bridge foundations scour evaluation.•Hydrological modeling incorporates model uncertainty by using an aver-aging approach.•Main flow characteristics are simulated with the open-source HEC-RAS model.•Bridge scour assessment takes advantage of HEC-RAS scour module.•Methodology can be potentially incorporated into regular bridge inspection schedules. The collapse of bridges inevitably leads to economical losses and may also be responsible for human fatalities. A bridge may fail due to several reasons, with local scouring around its foundation being the most common. Despite decades of scouring research, there are still many uncertainties affecting the design process of bridge piers. The most critical and least explored are the hydrological and hydraulic variables. The recent intensification of floods may also increase the vulnerability of bridges to scour effects. Therefore, the present work aims to propose a risk-based methodology for considering scour at bridge foundations. It is composed of three main steps: (i) assessing extreme hydrological events (hazards); (ii) modeling river behavior through the computation of flow characteristics and bridge scour depths; and (iii) assessing bridge scour risk by associating its scour depth to foundation depth ratio with the priority factor (vulnerability) and assigning a qualitative evaluation of the scour risk rating (level of risk). The hydrological modeling incorporates uncertainty with an averaging approach in the design floods definition. The flow characteristics are simulated with the HEC-RAS model, which also contains a scour module for bridge scour assessment. However, other empirical estimates are considered for simple and pile-supported foundations. This study ends with a qualitative assessment of how the scouring phenomenon affects bridge vulnerability and its safety. The proposed risk-based methodology - validated through a case study, the new Hintze Ribeiro bridge in Portugal - can be potentially incorporated into regular bridge inspection schedules as a useful tool for risk management measures, assisting in catastrophic events’ prevention.