For the difficulty of the traditional sounding method in shallow water areas，based on the composition and principle of the unmanned boat sounding system，we studied the influence of the attitude of the unmanned boat on the sounding，and the method of gross error detection and filtering of sounding data. The analysis shows that the influence of attitude in shallow water area on depth sounding is limited，and medium filtering method，weighted average method，and trend surface filtering method can be used to process the gross error of sounding data. Combined with the application of the actual project，it is proved that unmanned boat systems can meet the demand of shallow water channel surveys and the accuracy of sounding can meet the specification requirements，which can provide a reference for similar projects.