The multibeam echo sounder (MBES) data was collected from the 28.04.2019 (23:19 UTC) to the 07.05.2019 (16:42 UTC) with the Kongsberg EM122 on RV Maria S. Merian during the transit from Montevideo (Uruguay) to Las Palmas (Canary Islands, Spain) in the Southern Atlantic Ocean (MSM82/2). The deep-water MBES EM122 operates with an acoustic frequency of 12 kHz and a beam opening angle of 2° x 2°. The time, motion and position data (WGS84, geographic) was measured by the Kongsberg Seapath system on board. During the acquisition the echo sounder was monitored as well as settings and filter adjusted according to the environment. The swath opening angle was set between 65° and 70°. As the data was collected during transit, no specific survey was performed.Sound velocity profiles (SVP) were measured on the 01.05.2019 (XSV probe) and 04.05.2019 (with CTD) and applied in the MBES acquisition software SIS. To improve the bathymetric data before the first SVP measurement, an synthetic SVP extracted from the World Ocean Atlas 2009 (Levitus, 2013) using the software Sound Speed Manager (developed by the UNH Center for Coastal and Ocean Mapping and NOAA Coast Survey Development Laboratory (CSDL)). The SVP data is not part of this submission. The data was post-processed using the software QPS Qimera. No further SVP re-computation, navigation correction or tide correction was applied. Erroneous depth measurements were deleted manually by using the swath and slice editor. The vertical datum is mean sea level (MSL). The cleaned data was exported bathymetric grids in a resolution of 100 m (geotiff format, projected coordinates WGS84/UTM zone 23S (EPSG: 32723) to 26S (EPSG: 32726) and 26N (EPSG: 32626)). The coordinate system is indicated in the file name.