Geophysical exploration of archaeological sites has been a successful tool becoming more and more popular in the last decades. Many archaeological features can be detected with magnetic gradiometry (MGR), such as fire places, burned loam, metal artifacts, or other remnants, which produce a remanent magnetic signal detectable on the surface. However, as magnetic minerals are also present in natural settings, e.g. sedimentary and magmatic rocks and sediments derived from these host rocks, the MGR signal from archaeological artifacts is often embedded in a broader geomorphological signal, which makes separation of the different sources difficult. We provide geophysical data from two complex archaeological sites in northern Germany, which have been obtained with different methods, e.g. magnetic gradiometry (MGR), electrical resistivity tomography (ERT), electro-magnetic mapping (EM), and ground-penetrating radar (GPR). The combination of geophysical methods maps different material properties of both the geomorphological and the archaeological sources. We then use the three-dimensional modeling tool PREDICTOR to analyze the sources for the geophysical signals, e.g. the dominant signal in Leimbach, resulting from infill of palaeo-channels in the settlement area, and fire places as well as shafts in the hill fort of Lossow. The model prediction enables us to quantify the structures in the sub-surface and therefore helps to unravel complex situations often present in archaeological excavations.