Although barely known and poorly understood, submarine groundwater discharge (SGD) is a widespread phenomenon occurring at many coastal areas around the globe. In some coastal regions, where SGD represents a pathway for solute input from land into the sea it causes coastal pollution and eutrophication, respectively. This has been found for instance at some coasts off the New England States, where groundwater-borne nutrients even cause algal blooms. In other cases, particularly in karst areas, freshwater is released to the sea through submarine springs leading to a substantial loss of drinking water as commonly appearing at Mediterranean coasts like off Sicily, Greece, and Turkey. Against the background of increasing global drinking water shortage, submarine freshwater reservoirs could become an important alternative to on shore aquifers in those areas. However, hitherto the awareness of SGD is rather small and, thus, knowledge about chances and risks associated with this phenomenon is poor. To a certain extend this is due to the difficult identification, localisation, and quantification of SGD. In contrast to time consuming sediment and water column sampling in situ sensors and acoustic survey techniques offer the opportunity of area-wide mapping in respect to physical anomalies associated with SGD. Carrying a variety of complementary acoustic and oceanographic tools on a very confined space makes Autonomous Underwater Vehicles (AUVs) ideally appropriate to survey small scale structures at the sea bottom as well as temperature and salinity anomalies caused by freshwater discharge.Here we report on an AUV survey recently performed at submarine freshwater seeps in Eckernförde Bay, Western Baltic. SGD has been relatively well characterised for this area by a multitude of ?classical? hydrogeological, geophysical, and geochemical pre-investigations. Such information provides a valuable reference for the data obtained by the AUV survey which is, to our knowledge, the first to investigate SGD.These surveys demonstrated the appropriateness of AUVs to localize and quantify SGD by acoustic mapping and oceanographic sensing. Beside the increasing variety of acoustic tools, future development of different kinds of chemical and oceanographic real time sensors to be carried by AUVs will allow efficient multidimensional water column and remote seafloor surveys of high temporal and spatial accuracy.