Abstract: In order to measure the depth of water and ensure the safety of navigation, dual-frequency GNSS receiver with dual-frequency depth sounder were used. GNSS RTK technology and navigation sounding software are used to collect plane and depth data. Underwater topographic monitoring and tracking analysis of Artificial Maintenance Section and Harbour Waters were carried out in Yangshan Deepwater Port. All records, calculations and accuracy indicators meet the requirements of the standards, and the measurement results arereliable. The current situation of waterway, the tendency of water depth and the river bed changing are obtained, which provides a preliminary reference for dredging. The safety for the normal navigation of Yangshan Deepwater Port is guaranteed.