Bathymetric surveys performed using small, unmanned vessels are increasingly used in coastal areas and regions difficult to access by hydrographic motorboats. Their geometric dimensions, manoeuvring parameters, low labour intensity, and costs of survey execution have allowed the unmanned survey vessel (USV) to be a commonly recognised surveying platform. It is equipped with a navigation system for positioning, maintaining a course or survey line, determining spatial orientation, and measuring depths. The operation zone of the global navigation satellite system (GNSS) in coastal water regions enables geodetic positioning in land-based surveys and of moving objects, also including, for example, a sounding vessel. Under difficult observational conditions, the positioning is limited by the obscuration of the upper hemisphere, i.e., the visibility of satellites and the reflection from high field buildings. This poses a threat to a small vessel operating at a very short distance from a hydro-engineering structure. Based on a study performed in a marina, the article presents the determination of the minimum safe distance of the planned survey line to the quay in terms of the USV’s dimensions under good sounding conditions. These include low and constant velocity and good observational conditions for a GNSS receiver. The analysis was conducted on survey lines perpendicular to the quay, which was approached twice at distances of 1–5 m, with a 0.5 m interval. A 1 m distance between the end of the survey line and the quay has been determined for the safety of USV’s navigation and continuity of geospatial data collection during bathymetric surveys.