The cross-border correlations of the Miocene lithostratigraphic units (Slovakia, Austria) remain poorly constrained, owing to the various sources of clastic material transported into the basin and the low stratigraphic resolution of conglomerates. Therefore, this study is focused on the Lower and Middle Miocene conglomerates in the deltaic systems of the northern Vienna Basin and assesses their implications for cross-border correlations, as well as for the evolution of the Eastern Alpine–Western Carpathians junction area. Revision of lithostratigraphy is based on analyses of the Zohor-1 and Lozorno-1 wells, including the reassessment of published data to account for any refined geochronology and paleogeography. The Lower Miocene Jablonica deltaic system is formed by deposits originating in the alluvial, deltaic, and littoral environments in the basin’s northernmost tip. The conglomerates of exclusively Western Carpathian provenance pass into the deep-water marine mudstones of the Ottnangian Lužice and Karpatian Lakšáry fms. The Karpatian conglomerates at the base of the Zohor-1 well can be correlated both with the conglomerates of the Jablonica deltaic system in the north, as well as with the conglomerates of the Gänserndorf Mb. in the south. The overlying heterolithic flood plain of the deltaic sediments from the Závod Fm. most likely form the facies continuation of the alluvial to flood plain deposits of the Schönkirchen Mb. (upper part of the Aderklaa Fm.). The Middle Miocene deposition starts with terrestrial sediments along the slopes of the Malé Karpaty Mts. dated to 15.2 Ma. Later, along with the Devínska Nová Ves fan-delta, the presence of Orbulina suturalis developed in the marginal parts of the Vienna Basin during the Early Badenian. Despite having the same structural position, it is younger than the Rothneusiedl Formation in the southern part of the Vienna Basin. The provenance of clastics reflects the source in the Central Western Carpathian units and documents the Miocene uplift of the horst structure of the Malé Karpaty Mts.