The ability to ensure the resiliency and to predict the future performance of coastal bridges is very dependent on identifying damages in critical components of the bridge rapidly after an event. Traditional vibration based damage detection efforts focused mainly on the detection of fatigue cracking. Although detecting fatigue cracking is important, it does not contribute significantly to the total number of bridge failures in the United States. A critical review of the up-to-date literature showed that hydraulic loading, including scour, is responsible for about 50% of the failed bridges over the period of 1989–2000. To this end, the primary focus of this research is the development and evaluation of damage detection techniques capable of rapidly identifying and possibly quantifying the extent of deterioration of critical coastal bridges due to scour at submerged piers without underwater instrumentation. This paper illustrates, for the first time, the use of horizontally-displaced mode shapes and the calculated change in the dynamic flexibility features to identify scour from the response of the bridge superstructure.