In the area of Bad Deutsch-Altenburg (Hainburg Mountains, Lower Austria) a Middle Miocene transgression over Mesozoic basement was explored in the course of the Danube power plant project “Hainburg”. The Mesozoic basement forms a narrow ridge dipping to the northeast towards the Vienna Basin, covered by various Miocene sediments. The ridge represents a specific paleotopography that required a detailed study with 78 shallow, fully cored drill holes in an area of c. 0.5 km2. Ten drillings were selected for this study based on sedimentary composition and position relative to the Mesozoic ridge. These 10 cores, ranging in drilling depth from 26.5 to 96.4 m, were studied in respect to sedimentology, corallinacean algae, calcareous nannoplankton, foraminifers and ostracodes to reconstruct sediment distribution and paleoenvironment. Sediment distribution clearly shows that the Mesozoic ridge formed a physical barrier with siliciclastics dominating in the SW of the ridge and carbonate sediments prevailing in the NE. Based on biostratigraphy (calcareous nannoplankton, foraminifera, ostracodes, dinoflagellates) the majority of the sediments can be dated to the late Badenian (early Serravallian) only in some drillholes lower Sarmatian (upper Serravallian) sediments were detected. In terms of sequence stratigraphy, the Badenian sediments represent the transgressive and highstand systems tract of 3rd order sequence TB 2.5 (bound by the lowstands Ser 2 and Ser 3), the lower Sarmatian sediments can be correlated to sequence TB 2.6. Carbonate sediments show a wide spectrum of 13 facies which are mostly dominated by coralline algae. According to the relative positions of the drill holes a water depth between 0 and about 50 m can be reconstructed what is supported by the occurrence of the benthic biota. This biota indicates that the sedimentary succession started from the very beginning under full marine conditions. Except of basal conglomerates/breccias water energy conditions were low and turbidity high. Close to the Sarmatian boundary a reduction in salinity and depth may have occurred which is also observed in the Sarmatian sediments. Carbonate sediments and, in particular, larger benthic foraminifers indicate tropical to warm-temperate conditions for the late Badenian of the studied sections. The siliciclastic sediments NW of the Mesozoic ridge reflect riverine input indicated by the occurrence of freshwater ostracodes and characean oogonias. Calcareous nannoplankton and dinoflagellates show a high share of reworking from Upper Cretaceaous and Paleogene sediments.