Abstract: According to the Helsinki Commission report from 1994 around 15000 tonnes of chemical warfare agents were dumped to the Baltic Sea after World War II as part of the demilitarization process of the former Nazi Germany. Continuing corrosion of metal encasements makes the dumped munitions a ticking time-bomb, which could potentially harm the whole Baltic Basin. The presented work addresses important aspects for a proper evaluation of the threat; side scan sonar survey data storage and analysis of a spatial distribution of the sonar targets potentially related to chemical weapons. The chosen software environment was GIS oriented. ESRI ArcGIS built-in tools were used to determine the hotspots of the targets on the official post-war munitions dumping sites; Gotland Deep and Bornholm Deep. The automation process of mapping in GIS was also proposed. Therefore, a holistic approach for digital mapping of the sonar targets related to dumped munitions was created.