Lacking substructure information usually challenges bridge agencies when evaluating the flood or earthquake resistance of bridges in disaster-prone areas. Appropriate substructure inspection techniques are essential for bridge engineers to develop repair strategies efficiently and reasonably allocate maintenance funds. In this article, the electrical resistivity tomography technique was introduced to the foundation inspection of a rail bridge in Taiwan. Different survey layouts were chosen to inspect the pile bent substructures. Initially, the investigation line parallel to the traffic direction indicated an unexpected substructure pattern. Such a shallow low-resistivity anomaly crossing over more than ten pile bents severely interfered with the foundation depth inspection. Using two alternative investigation lines perpendicular to the previous survey direction successfully separated this low-resistivity zone into two single parts. One deeper low-resistivity contour located right below bridge position was identified as the foundation depths. Another shallow vertical-shape low-resistivity zone was identified as abandoned temporal sheet piles. This investigation case also reveals that two survey lines in different directions are suggested to separate the target substructure from unexpected embedded anomalies effectively.