A bio-inspired bridge structural health monitoring (SHM) system to evaluate the scouring depth of bridges by measuring the dynamic response of superstructure only is developed. The main objective of this research is develop an effective bridge SHM system to meet the urgent necessity of monitoring the large amount of old and aging bridges in the world. To solve the unique and complicated problem, the dynamic scouring effect is carefully considered in the bio-inspired bridge SHM system. The array expression data format is proposed for the development of the SHM algorithm to transplant the Deoxyribonucleic acid (DNA) array concept from molecular biology to the field of SHM. A two-tier auto-regression with exogenous (AR-ARX) process is used to extract the expression array from the recorded ambient vibration response. The scouring depth of the bridge is then determined by the proposed SHM algorithm based on Naïve Bayes (NB). To verify the performance and reliability of the SHM algorithm, a series of experiment on a scaled down single-column bridge model with dynamic scour impact under flooding was conducted with various settings of initial scour depth to clarify the complicated fluid-solid-coupling effect. Test results from the dynamic flooding test showed that the scouring depth of the bridge can be reliably identified by the proposed SHM system. The performance of the bio-inspired bridge SHM system has been successfully demonstrated.