This paper describes a three-dimensional ground penetrating radar (GPR) survey carried out around a levee of the Ara River in Saitama, Japan, where deformation of the ground was observed after heavy rainfall associated with the typhoon of September 2007. The high-density 3D GPR survey was conducted as a series of closely adjacent four directional sets of 2D surveys at an area surrounding vertical cracks on the paved road caused by deformations induced by heavy rain. The survey directions of the 2D surveys were 0, 90, 45, and -45 degrees with respect to the paved road and the intervals between lines were less than 0.5 m. The 3D subsurface structure was accurately imaged by the result of data processing using Kirchhoff-type 3D migration. As a result, locations and vertical continuities of the heavy rainfall induced cracks in the paved road were clearly imaged. This will be a great help in considering the generation mechanisms of the cracks. Moreover, the current risk of a secondary disaster was found to be low, as no air-filled cavities were detected by the 3D GPR survey.