This integrated study of the sedimentology, magnetostratigraphic chronology and petrography of the mostly continental clastics of the Oligocene to Miocene Swiss Molasse Basin underpins a reconstruction of facies architecture and delineates relationships between the depositional evolution of a foreland-basin margin and exhumation phases and orogenic events in the adjacent orogen. A biostratigraphically based high-resolution magnetostratigraphy provides a detailed temporal framework and covers nearly the whole stratigraphic record of the Molasse Basin (31.5–13 Ma). Three transverse alluvial fan systems evolved at the southern basin margin. They are characterized by distinct petrographic compositions and document the exhumation and denudation history of the growing eastern Swiss Alps. Enhanced northward propagation of the orogenic wedge is interpreted to have occurred between 31.5 and 26 Ma. During the period 24–19 Ma, intense in-sequence and out-of-sequence thrusting took place as Molasse strata were accreted to the orogenic wedge. A third active tectonic phase, possibly caused by backthrusting of the Plateau Molasse, probably occurred between ca. 15 and 13 Ma. Fan head migration between 31.5 and 13 Ma is probably controlled by the structural evolution of the thrust front due to Molasse accretion and backthrusting.