Plitvice Lakes National Park is the largest national park in Croatia and also the oldest from 1949. It was added to the UNESCO World Natural Heritage List in 1979, due to the unique physicochemical and biological conditions that have led to the creation of 16 named and several smaller unnamed lakes, which are cascading one into the next. Previous scientific research proved that the increased amount of dissolved organic matter (pollution) stops the travertine processes on Plitvice Lakes. Therefore, this complex, dynamic but also fragile geological, biological and hydrological system required a comprehensive limnological survey. Thirteen of the sixteen lakes mentioned above were initially surveyed from the air by an unmanned aircraft equipped with a survey grade GNSS and a full frame high-resolution full-screen camera. From these recordings, a georeferenced, high-resolution orthophoto was generated, on which the following surveys by a multibeam sonar depended. It is important to mention that this was the first time that these lakes had ever been surveyed both with the multibeam sonar technique and with such a high-resolution camera. Due to the fact that these thirteen lakes are difficult to reach and often too shallow for a boat-mounted sonar, a special autonomous surface vehicle was developed. The lakes were surveyed by the autonomous surface vehicle mounted with a multibeam sonar to create detailed bathymetric models of the lakes. The missions were planned for the surface vehicle based on the orthophoto from the preliminary studies. A detailed description of the methodology used to survey the different lakes is given here. In addition, the resulting high-resolution bathymetric maps are presented and analysed together with an overview of average, maximum depths and number of data points. Numerous interesting depressions, which are phenomena consistent with previous studies of Plitvice Lakes, are noted at the lake beds and their causes are discussed. This study shows the huge potential of remote sensing technologies integrated into autonomous vehicles in terms of much faster surveys, several orders of magnitude more data points (compared to manual surveys of a few decades ago), as well as data accuracy, precision and georeferencing.