To improve the positioning ability of shipborne underwater acoustic equipment in complex operating environments of port and waterway engineering，this paper investigates the components of the shipborne position and orientation system for marine vessels (POS MV) and the basic principle of integrated global navigation satellite systeminertial navigation system (GNSSINS) positioning by the onboard Applanix IN-Fusion.Specifically，it develops four kinds of mode selection strategies for POS data post-processing and the procedures of corresponding methods on the basis of POSPac MMS and fosters the core technology system for shipborne POS data acquisition and processing.Then，relying on the scanning survey project of the Wenling Waterway dredging project，the paper presents the engineering practice of POS MV WaveMaster data acquisition and processing conducted 35 km offshore for 2.17 h.The results suggest the following conclusions：1) In the case of non-satellite difference，the real-time plane and elevation positioning accuracy of POS MV are both at meter level，and its average roll，pitch，and heading positioning accuracy are 0.026°，0.026°，and 0.029°，respectively.2) In the Post-processing Real Time eXtended (PP-RTX) and SingleBase post-processing modes of POSPac MMS，the plane and elevation positioning accuracy increase to 2-3 cm，and the average roll and heading positioning accuracy rise to 0.012° and 0.015°，respectively，with a stable mean square error in true heave data of 0.01 m.3) POS MV can obtain stable and effective inertial navigation data in real time，and auxiliary post-processing technology can provide accurate position and attitude information for port and waterway engineering.