In the last decade, paleoseismological studies executed in northern Germany have extended the record of fault activity further into the past, partly leading to controversial discussions. Although it has been possible to identify GIA as a potential key trigger mechanism for the neotectonic, historic and recent fault activity in northern Germany, the major controlling factors for the distribution of tectonic activity are still underexplored. We investigate the basin-fill architecture and subsidence mechanisms of the Lehringen basin as a key example of an important Eemian archaeological archive. Based on the interpretation of shear-wave seismic sections, a ground penetrating radar (GPR) survey, borehole data, DEM analyses and numerical simulations of Coulomb failure stress, we assume that Eemian and Weichselian sediments near Lehringen were deposited in small fault-related basins that formed as a consequence of neotectonic movements along the Aller fault system. Two phases of subsidence can be derived, based on the seismic sections and the GPR survey, which points to two phases of fault activity after the late Saalian glaciation. This supports the idea that the Aller fault system is a glacially triggered fault and indicates that two separate phases of fault activity might have occurred. The identification of neotectonic activity on the Aller fault system has implications for a future seismic hazard assessment of Northern Central Europe and the definition of seismo-tectonic areas.