Bridge pier foundations occasionally become unstable due to scouring around piers in flood conditions, and operational restrictions imposed according to the water level are practical for maintaining safe train operation. However, when such restrictions are lifted, it is quite difficult to verify the condition of the bridge pier foundation. It is therefore necessary to develop a practical method of quantitatively evaluating and assessing the structural integrity of bridge pier foundations in flood conditions. This paper reports the results of analysis of long-term microtremor measurements made on existing bridge piers and a method to define the natural frequencies of bridges using microtremors.