Abstract. The stratigraphic architecture of the Swiss Molasse basin, situated on the northern side of the evolving Alps, reveals crucial information about the basin's geometry, its evolution, and the processes leading to the deposition of the siliciclastic sediments. Nevertheless, the formation of the Upper Marine Molasse (OMM) and the controls on the related Burdigalian transgression have still been a matter of scientific debate. During the time period from ca. 20 to 17 Ma, the Swiss Molasse basin was partly flooded by a shallow marine sea striking SW–NE. Previous studies have proposed that the transgression occurred in response to a rise in global sea level, a reduction of sediment flux, or an increase in tectonically controlled accommodation space. Here, we readdress this problem and extract stratigraphic signals from the Burdigalian molasse deposits that can be related to changes in sediment supply rate, variations in the eustatic sea level, and subduction tectonics. To achieve this goal, we conducted sedimentological and stratigraphic analyses of several sites across the entire Swiss Molasse basin. Field investigations show that the transgression and the subsequent evolution of the Burdigalian seaway was characterized by (i) a deepening and widening of the basin, (ii) phases of erosion and non-deposition during Lower Freshwater Molasse (USM), OMM, and Upper Freshwater Molasse (OSM) times, and (iii) changes in along-strike drainage reversals. We use these changes in the stratigraphic record to disentangle tectonic and surface controls on the facies evolution at various scales. As the most important mechanism, rollback subduction of the European mantle lithosphere most likely caused a further downwarping of the foreland plate, which we use to explain the deepening and widening of the Molasse basin, particularly at distal sites. In addition, subduction tectonics also caused the uplift of the Aar massif. This process was likely to have shifted the patterns of surface loads, thereby resulting in a buckling of the foreland plate and influencing the water depths in the basin. We use this mechanism to explain the establishment of distinct depositional settings, particularly the formation of subtidal shoals wherein a bulge in relation to this buckling is expected. The rise of the Aar massif also resulted in a reorganization of the drainage network in the Alpine hinterland, with the consequence that the sediment flux to the basin decreased. We consider this reduction in sediment supply to have amplified the tectonically controlled deepening of the Molasse basin. Because the marine conditions were generally very shallow, subtle changes in eustatic sea level contributed to the formation of several hiatuses that chronicle periods of erosion and non-sedimentation. These processes also amplified the tectonically induced increase in accommodation space during times of global sea level highstands. Whereas these mechanisms are capable of explaining the establishment of the Burdigalian seaway and the formation of distinct sedimentological niches in the Swiss Molasse basin, the drainage reversal during OMM times possibly requires a change in tectonic processes at the slab scale, most likely including the entire Alpine range between the Eastern and Central Alps. In conclusion, we consider rollback tectonics to be the main driving force controlling the transgression of the OMM in Switzerland, with contributions by the uplift of individual crustal blocks (here the Aar massif) and by a reduction of sediment supply. This reduction of sediment flux was likely to have been controlled by tectonic processes as well when basement blocks became uplifted, thereby modifying the catchment geometries. Eustatic changes in sea level explain the various hiatuses and amplified the deepening of the basin during eustatic highstand conditions.