Regarding the requirements of high precision bathymetry in waterway engineering，this paper takes the single-beam bathymetry system as the research object and introduces the bathymetry principle and main influencing factors of bathymetric errors. Moreover，this paper analyzes the main error sources of high precision bathymetry from the perspectives such as positioning errors，bathymetric errors，water level errors，and environmental effects and puts forward corresponding reduction measures，which are subsequently verified by experiments. We recommend using RTK three-dimensional bathymetry technology to eliminate the influence of water level errors，correcting the navigation delay to reduce the influence of positioning errors，and utilizing attitude sensors to remove the influence of roll and pitch attitude angles on bathymetric errors. Finally，the influence of errors in the bathymetry process is reduced，and the accuracy of bathymetry is improved.