Structural health monitoring (SHM) is one of the main research topics in civil, mechanical and aerospace engineering. In this regard, modal parameters and their trends over time can be used as features and indicators of damage occurrence and growth. However, for practical reasons, output-only techniques are particularly suitable for the system identification (SI) of large civil structures and infrastructures, as they do not require a controlled source of input force.In this context, these approaches are typically referred to as operational modal analysis (OMA) techniques. However, the interpretation of the OMA identifications is a labour-intensive task, which could be better automated with artificial intelligence and machine learning (ML) techniques. In particular, clustering and cluster analysis can be used to group unlabelled datasets and interpret them. In this study, a novel multi-stage clustering algorithm for automatic OMA (AOMA) is tested and validated for SHM applications-specifically, for damage detection and severity assessment-to a masonry arch bridge. The experimental case study involves a 1:2 scaled model, progressively damaged to simulate foundation scouring at the central pier.