The approach in archaeological research today is to fully utilize non invasive methods and technologies for data collection. In marine or underwater archaeology most of the procedures in the so called remote sensing field comes from acoustic sensors or sonar technology. In the past decade a vast hydrographical data was more or less systematically collected for different purposes in Slovenian sea and inland waters. These include bathymetric single-beam and multi-beam data, side scan sonar data of coastal belt and sporadic sub-bottom profiler data. Among these, bathymetric data especially multi-beam echo-sounder (MBES) data, stands out as being the most precise and complete. Archaeological applications of MBES are diverse and depend mainly on the deployment vessel, water depth and the system used. On the one hand it can be applied as precise tool to map surface structures of underwater sites and on the other hand as tool for general prospection of extensive areas in order to discover new sites with archaeological potential. Bathymetric data also represents a good starting point for any further geophysical prospection. The focus of this paper will be on MBES and parametric sub-bottom data with case studies that demonstrate why acoustic prospection is an essential part of any research in underwater archaeology.