Underwater cultural heritage sites are subject to constant change, whether due to natural forces such as sediments, waves, currents or human intervention. Until a few decades ago, the documentation and research of these sites was mostly done manually by diving archaeologists. This paper presents the results of the integration of remote sensing technologies with autonomous marine vehicles in order to make the task of site documentation even faster, more accurate, more efficient and more precisely georeferenced. It includes the integration of multibeam sonar, side scan sonar and various cameras into autonomous surface and underwater vehicles, remotely operated vehicle and unmanned aerial vehicle. In total, case studies for nine underwater cultural heritage sites around the Mediterranean region are presented. Each case study contains a brief archaeological background of the site, the methodology of using autonomous marine vehicles and sensors for their documentation, and the results in the form of georeferenced side-scan sonar mosaics, bathymetric models or reconstructed photogrammetric models. It is important to mention that this was the first time that any of the selected sites were documented with sonar technologies or autonomous marine vehicles. The main objective of these surveys was to document and assess the current state of the sites and to establish a basis on which future monitoring operations could be built and compared. Beyond the mere documentation and physical preservation, examples of the use of these results for the digital preservation of the sites in augmented and virtual reality are presented.