The bathymetric surveys executed with a use of small survey vessels in limited water areas, including offshore areas, require precise determination of the geospatial coordinates of the seabed which is a synthesis of, among others, determining the position coordinates and measuring the depth. Inclination of the seabed and the declining depth make manoeuvring of the sounding vessel, e.g., a hydrographic motorboat or Unmanned Survey Vehicle (USV), in shallow water impossible. Therefore, it is important to determine the minimal depth for the survey resulting from the draught of the sounding vessel and the limits of the sounding area. The boundaries also result from the dimensions of the sounding vessel, its manoeuvring parameters and local water level. Type of the echosounder used in the bathymetric survey is a decisive factor for the sounding profile planning and the distances between them and the survey vessel for the possibility performing the measurements in shallow water. Electronic Navigational Chart (ENC) was used to determine the water area’s boundaries, and the safety contours were determined on the basis of the built Digital Sea Bottom Model (DSBM). The safety contour, together with the vessel’s dimensions, its manoeuvring parameters and the hydrometeorological conditions, limit the offshore area in which the measurement can be performed. A method of determining boundaries of the survey performed by a USV equipped with SingleBeam EchoSounder (SBES) on survey lines perpendicular to the coastal line are presented in the paper in order to cover the water area with the highest amount of measurement data, with the USV’s navigational safety taken into consideration. The measurements executed on the municipal beach served verification of the DSBM.