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The transition zone between Eastern Alps and Pannonian Basin is a key area for the investigation of the interplay between regional uplift, local tectonic subsidence and depositional environment. Our study area, the western margin of the Little Hungarian Plain, is characterized by gentle hills, plateaus and depressions, of which several are filled by lakes—including one of Austria’s largest and shallowest lakes, Lake Neusiedl. Geological investigation is hampered by the scarcity of outcrops, and thus direct observation of sedimentological or structural features is difficult. Despite a long research history in the area, a consistent landscape evolution model considering all relevant constraints is lacking so far. In this study, we apply multidisciplinary methods to decipher the complex tectonic and fluvial depositional evolution of the region. Local data from shallow-lake drilling and seismic investigation are combined with regional data from industrial seismics and core data to gain new insights into the latest Pannonian (Late Miocene) and Quaternary evolution. Shallow-lake seismic data show the erosionally truncated Pannonian sediments dipping and thickening toward southeast, toward the modern depocenter of the Little Hungarian Plain. Overlying Quaternary fluvial sediments show a very similar thickening trend except for the area on the plateau north of the lake indicating ongoing subsidence in major parts of the basin. Drill cores from locations along the lake seismic lines were analyzed concerning their age, mineralogy and heavy minerals and compared with outcrop samples from the surrounding plains and the plateau to derive indications on sediment provenance. A key observation is the apparent lack of a significant gravel layer on top of the tilted Pannonian sediments beneath Lake Neusiedl. Small-scale faults can be observed in the lake seismic sections along with key sedimentary features. Significant differences of the current elevation of the top Pannonian between the surrounding plains and the plateau indicate post-Pannonian normal faulting, which is a key process in shaping the present-day morphology of the region. Luminescence ages of samples from the Quaternary fluvial gravels on top of the Pannonian sediments are a significantly higher (>300 ka) compared to the gravels in the plain (102 ± 11 and 76 ± 8 ka), suggesting ongoing tectonic subsidence. © 2016, Springer-Verlag Berlin Heidelberg.