The rising sea levels caused by the climate crisis are causing significant changes in the coastal environment of the Korean Peninsula, leading to increased demand for coastal erosion protection. Accurate bathymetric information is crucial for implementing effective prevention measures. However, existing methods such as the airborne light detection and ranging (LiDAR) bathymetry (ALB) and multibeam echo sounder (MBES) are not cost-effective for small-scale regions, and the single-beam echo sounder (SBES) method using manned survey vessels is challenging to use in low-water-depth areas. In this study, we aimed to develop an autonomous surface vehicle (ASV) to conduct bathymetric surveying at a very small water depth of less than 2.0 m. The survey was conducted by connecting SBES and network real-time kinematic (N-RTK) positioning data to a small, self-developed ASV. The vessel was autonomously navigated using N-RTK positioning data during most measurement operations, allowing for precise sounding intervals using a simple waypoint setting for each planned sidetrack without direct steering. The bathymetric measurements of exposed or partially exposed rocks at average water depths of 2.0 m or less could be obtained from the bathymetric surveying using the unmanned vessel and devices applied in this study.