Bathymetry is a subset of hydrography, aimed at measuring the depth of waterbodies and waterways. Measurements are taken inter alia to detect natural obstacles or other navigational obstacles that endanger the safety of navigation, to examine the navigability conditions, anchorages, waterways and other commercial waterbodies, and to determine the parameters of the safe depth of waterbodies in the vicinity of ports, etc. Therefore, it is necessary to produce precise and reliable seabed maps, so that any hazards that may occur, particularly in shallow waterbodies, can be prevented, including the high dynamics of hydromorphological changes. This publication is aimed at developing a concept of an innovative autonomous unmanned system for bathymetric monitoring of shallow waterbodies. A bathymetric and topographic system will use autonomous unmanned aerial and surface vehicles to study the seabed relief in the littoral zone (even at depths of less than 1 m), in line with the requirements set out for the most stringent International Hydrographic Organization (IHO) order—exclusive. Unlike other existing solutions, the INNOBAT system will enable the coverage of the entire surveyed area with measurements, which will allow a comprehensive assessment of the hydrographic and navigation situation in the waterbody to be conducted.