The Vienna based “Ludwig Boltzmann Institute for Archaeological Prospection and Virtual Archaeology”, in collaboration with the County of Upper Austria - Direktion Kultur, and the “Vienna Institute for Archaeological Sciences” of the University of Vienna, has in the past two years set up a unique high-technological research infrastructure for large-area high-resolution underwater prospection in shallow waters, extending the large-area archaeological prospection approach from land to shallow underwater sites. This infrastructure consists of a seaworthy cabin motorboat as survey platform with computer workstation, an ultra-high-resolution multibeam-sonar system including state-of-the-art software and sound velocity profilers, an innovative four-channel parametric sediment-sonar for sub-bottom profiling in very shallow water, as well as the necessary precise data positioning system. As first case studies, the UNESCO World Heritage pile dwelling sites in the Upper Austrian lakes Mondsee and Attersee will be explored, mapped and documented using this novel prospection system in the framework of the textquotedblArchPro Oberösterreichische Pfahlbautentextquotedbl project (www.archpro.info). We will present technology, methodology and first results of the large-area application of this innovative underwater archaeological prospection approach.