In order to determine the maximum depth to be scoured during flooding at the narrow segment at the Iwadu point of the Yoshino River in Japan, we conducted a study to measure the thickness of the sediment layer using a narrow multi-beam and a sub-bottom profiler. The sub-bottom profiler detected a consolidated silt layer at a depth of approximately 10 m below the riverbed. Results from a boring survey conducted at three different points for verification, found that the N value changed sharply at this layer, where estimates indicated the deepest riverbed level historically recorded. In addition, it was nearly the same value with the calculated bed level during the largest discharge condition in the past by the quasi-three dimensional flow analysis.