Marine benthic systems are particularly impacted by human-induced stresses and management strategies are urgently needed to maintain their important ecosystem processes. In the Baltic Sea, effective administrative measures are often hampered by the lack of knowledge regarding the distribution and structure of certain benthic biotopes. In this thesis, information about under-explored rock habitats in offshore and deeper waters of the German Baltic Sea were gained by the use of a novel seafloor imaging system. Allowing to sample on complex terrain, at broad spatial scales and without extraction of specimen, the system was first deployed on hard substrata in the ‘Fehmarn Belt’. After successful exploration of the local communities, the system was consecutively used on all major rock habitats in the German Baltic exclusive economic zone. Assemblage structure was assessed and spatial patterns were linked to environmental drivers. Finally, the imaging system was deployed in the central Arkona basin to characterize a recently discovered boulder reef for the very first time.