The performance of bathymetric measurements by traditional methods (using manned vessels) in ultra-shallow waters, i.e., lakes, rivers, and sea beaches with a depth of less than 1 m, is often difficult or, in many cases, impossible due to problems related to safe vessel maneuvering. For this reason, the use of shallow draft hydrographic Unmanned Surface Vessels (USV) appears to provide a promising alternative method for performing such bathymetric measurements. This article describes the modernisation of a USV to switch from manual to automatic mode, and presents a preliminary study aimed at assessing the suitability of a popular autopilot commonly used in Unmanned Aerial Vehicles (UAV), and a low-cost multi-Global Navigation Satellite System (GNSS) receiver cooperating with it, for performing bathymetric measurements in automated mode, which involves independent movement along a specified route (hydrographic sounding profiles). The cross track error (XTE) variable, i.e., the distance determined between a USV’s position and the sounding profile, measured transversely to the course, was adopted as the measure of automatic control precision. Moreover, the XTE value was statistically assessed in the publication.