Abstract: Data obtain during sounding Gdańsk Bay with SES-2000 Standard parametric sub-bottom profiler has two types of information: envelope and pure signal. First is used to plot echograms in real time and contain envelope of echo. The second one is stored during sounding and can be processed after recording data. Comparison of results will be shown and discussed. First step in investigation was proper configuration of small measurement vessel detailing localization of echosounder antennas and perypherical units (GPS, heading, motion sensor MRU-Z and navigation devices) complementing information of measurement system. There are different types of research (for example looking for buried objects or investigation of sediments layers) which require separate configuration of software working with sub-bottom profiler. Various settings will be presented and interrelated with real data. Very important in work with stored sounding data is proper post-processing realized with software dedicated to parametric echosounder SES2000 standard and Matlab which give possibility of clear presentation in 3D with precise measurement methods what will be presented on echograms coming from works on sea in 2009 year.