Recent studies have shown that the most common failures in bridges in Ecuador are due to river flooding, with flooding and scouring responsible for approximately 50% of collapses. This water-structure interaction directly affects substructures, altering their behavior and ability to transmit loads to the ground. This study evaluates the impact of water-structure interaction on the substructures of a reinforced concrete arch bridge located on Miguel de Unamuno Avenue in Azogues (Ecuador), which was severely affected by the flooding of the Burgay River in April 2022. Using an integrated Structural Health Monitoring (SHM) methodology, visual inspections, operational modal analysis (OMA) with five Raspberry Shake RS4D triaxial accelerometers, MASW geophysical prospecting, bathymetry with bottom sonar, and numerical modeling calibrated in SAP2000 were combined. The results showed maximum scouring of 3.85 m, a 48% loss of the effective bearing area of the footing, a 2.8° rotation of the right abutment, and a 21.3% reduction in the fundamental natural frequency, equivalent to an overall stiffness loss of 35–40%. The updated numerical model reproduced the experimental frequencies with an error of < 2%, confirming that scouring and loss of lateral soil confinement are the dominant mechanisms of degradation. It is concluded that SHM allows for the detection and quantification of damage induced by hydrological phenomena with high precision, the establishment of alarm thresholds, and the justification of urgent reinforcement interventions. The results provide a solid technical basis for implementing continuous monitoring on Andean bridges vulnerable to extreme events, promoting preventive management of road infrastructure in Ecuador.