The Němčice site located in a strategic area of an agricultural plateau represents one of the most important archaeological sites in Moravia. Non-destructive archaeological surveys including a largescale magnetometer survey, field artefact collections, and metal detector surveys have been carried out there repeatedly over the past two decades. New archaeological excavations during a new project were focused on selected areas and situations identified during magnetometer prospection. The results of an archaeological investigation of the site using test pits confirmed settlement, glass-making and ritual activity under magnetic anomalies at the site. The new possibility of comparing uncovered sunken features and distributions of magnetic anomalies provided new feedback for a more precise interpretation of similar anomalies from magnetograms. An additional detailed apparent magnetic susceptibility measurement in situ showed another possibility for the application of the geophysical method during archaeological excavations. We were able to obtain additional information about the fills or possible post-depositional processes of various sunken features in the case of vertical profiles monitored by magnetic susceptibility meter measurements. The use and combination of various geophysical data has been beneficial in the case of an archaeological site as important as Němčice, and will continue to be so in future archaeological research of the site.