We present the bathymetric dataset of a single beam sounding. Surveys were conducted in 25 expeditions of the Atlantic branch of Shirshov Institute of Oceanology RAS in the Russian EEZ area of the southeastern part of the Baltic Sea in the period from 2004 to 2018. Acoustic data were acquired by echo sounders Simrad EA-400SP and Furuno FS-700. The raw sounding data were filtered and corrected by sound velocity values. The dataset is presented as spreadsheets (*.xslx) and GIS point-class shapes (*.shp). The digital elevation model (DEM) of 1: 500 000 scale has been constructed for the entire Russian EEZ on base of the original array of sounding profiles and an open sources bathymetry [1]. DEM is presented by XYZ-grid (*.txt) and GeoTIFF raster (*.tif).