For the Palmer mechanical scanning pattern of an airborne laser bathymetry system, the potential errors of the scanning system are analyzed, and the associated error model is derived. The model composes the description of laser rays, water surface fluctuations, and refraction, and introduces certain simplifications concerning the water surface and column. Based on the scanning error model, the impact of each error source on the vertical and horizontal positioning accuracy is investigated and established through a numerical simulation. The quantitative impacts of each inaccuracy on the coordinates of the laser footprints on the sea surface and bottom were calculated, with a height of 100 m for the airborne platform and a water depth of 10 m. To verify the correctness of the simulation results and the error model based on a theoretical analysis, experiments are utilized with the system that we developed. Both the simulation analysis and experimental results show that this method can effectively obtain the systematic errors. The outcomes of the error model and analysis will give the theoretical foundations for lowering the effect brought on by each error source in the compensation scanning system and improving the point cloud accuracy in the ensuing data processing.