The constraint boundaries and dynamic characteristics of the bridge structures across the water region will change after the flood-induced scour. In order to investigate the effect of flood-induced pier and abutment scour on seismic performances of bridge components and the entire structure, a case study of an RC bridge engineering across a river in an earthquake-prone region of western China was conducted. The probabilistic statistical analysis was performed on the flood risk of the river based on the historical hydrological data of the river that across the case-study bridges. By developing the risk assessment curves of flood-induced scour depth for the pier and abutment, flood-induced scour conditions were characterized as severe, moderate, and typical using exceedance scour depth of probability 2%, 50% and 98%, respectively. In this context, the modeling methods of pile-soil-interaction and abutment-soil-interaction under three different scour conditions were discussed. A nonlinear finite element model of the case-study bridge was developed using the OpenSees program. Then, 100 seismic waves were inputted for dynamic response calculation of the bridges. Based on the calculated results, the influences of flood-induced pier and abutment scour on component and system fragility of the bridges, as well as the sequences of component damage, were investigated. The results show that with the increasing degree of flood-induced scour, the damage probability of the bridge pier gradually decreases, while that of the abutment and pile increases significantly. The damage probability of bearings increases but the change is not significant. In addition, the seismic fragility of the bridge structural system increases with increasing flood-induced scour degree. The damage sequence and grade difference of various bridge components also change significantly with increasing degree of flood-induced scour degree. In particular, the difficult-to-repair abutments and piles may be damaged first after the severe scour. The research results have significant practical engineering value for understanding the seismic performance of the RC bridges under the pier and abutment scour. Especially, it is necessary to consider the impact of pier and abutment scour during the operation phase of the bridges when designing the capacity protected members of the bridges across the water region. © 2024, Central South University Press. All rights reserved.