This multibeam echo sounder (MBES) bathymetry data and backscatter data, as well as subbottom profiler data, was acquired in Eckernförde Bay, Germany.The MBES data were acquired using an EM2040c system which was installed on R/V Alkor (Cruise AL447 - 2014). It operates with a 200-400 kHz transducer combined with a CodaOctupus F180 motion sensor. The survey was designed to provide high-resolution bathymetry with 0.5 x 0.5 m resolution. The bathymetry data were post-processed using sound velocity profiles acquired at regular intervals. Tidal corrections were applied using the tidal gauge in Eckernförde with reference to NHN, DHHN92.The backscatter amplitude data were corrected for the variation with grazing angle. We ensured the highest possible resolution by using the raw backscatter time-series data for each footprint (snippets) and compensated for the angle of incidence using reference grids.Subbottom profiler data were acquired with the R/V Alkor and R/V Elisabeth Mann Borgese in late October 2014 (cruise AL447), the beginning of July 2018 (cruise EMB187). The data were acquired using a parametric Innomar SES-2000 medium system creating secondary peak frequencies between 4 and 15 kHz.