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The effect of the rapid advancement of autonomous vehicles is the increase in their presence in various areas of the economy also in fields of defense. Autonomous submersible vehicles have been carrying out missions at large depths for many years, bringing the platforms to the vicinity of the measured object. At the same time, the use of surface vessels has been developing as support for bathymetric measurements in terms of work efficiency and cost reduction. The article presents results of a harbor survey performed with the use of, an autonomous, unmanned survey vessel, Teledyne Oceanscience Z-boat 1800 equipped with a compact MBES. Then, it compares the measurements with the data collected by conventional, manned hydrographic platforms fitted with both MBES and interferometric systems and draws attention to the aspects of bathymetric survey in which ASV vehicles show higher reliability.