In this research, we constructed a 3D riverbed surveying system that is able to acquire the topographical information of a riverbed in real-time. The system consists of a RTK-GPS receiver and a echo sounder for collecting simultaneously the position and the water depth information of riverbed. A program for data composition and transformation was designed to generate the 3D coordinates by combining data of a GPS receiver and a echo sounder and made GIS database construction easy. We extracted TIN, digital elevation model and cross sectional maps of the riverbed by using GIS software from 3D data constructed through test surveying. It was shown that the accuracy of the result was RMS error of 0.069m when compared with the existing methods which use a total station and staffs. It is expected that the 3D riverbed surveying system wiil be able to be utilized to various surveying for water resources management in rivers, sea, dams, storing reservoirs and so forth.