The underwater digital surface model (DSM) is of great importance for the characterization of the water-submerged zones. It has been noted that the effects of refraction at the air/water interface would cause the depth-dependent bias in the underwater DSM. In this study, we employ the empirical method, which gives the correction function based on the regression relation between the elevation of the river bed determined from the aerial image and that obtained from in-situ measurement. We use a medium frame camera, which attitude is determined by the onboard global positioning system and inertial measurement unit, with the pixel size of 6.8 μm and the ground resolution of 3 centimeters to acquire the high resolution color aerial imagery in northern Taiwan. The SOCET GXP software is used to carry out aerial triangulation. The results are compared with the in-situ measurements that were obtained by total station surveying (for depth < 40 cm) and single beam sonar (for depth > 40cm).