Aeolian dunes in the Moravian Sahara developed during at least two distinct cold periods of the Last Glacial Period (LGP). Their two-phase development was previously deduced solely from the different orientations of dune crests without knowing the dunes' internal structure. Therefore, the aim of this study is to reveal the internal structure of the multi-generational dune system, developing a relationship between these dunes and bedrock. A combination of data was obtained from boreholes and ground-penetrating radar (GPR). GPR profiles were measured in places where the boreholes were drilled to obtain high-resolution combination data. Furthermore, models of aeolian sediment thickness and ground-water level were made using a spatial interpolation method (ordinary kriging with spherical semivariogram model) to interpret the GPR results and to investigate a relationship between the bedrock and dune patterns. Internal dune structures confirm the hypothesis of multi-generational development of this dune field. In addition, the aeolian sediment distribution was influenced by the bedrock topography. Finally, this study confirms that a change in LGP atmospheric circulation over Central Europe is the main controlling factor in forming the Moravian Sahara dune field.