Abstract Changes in molluscan diversity across the 3rd order sequence boundary from the Lower to the Middle Miocene of the Paratethys were evaluated in the context of environmental bias. Taken at face value, quantitative data from nearshore and sublittoral shell beds suggest a transition from low-diversity Karpatian (Upper Burdigalian) to highly diverse Badenian (Langhian and Lower Serravallian) assemblages, but environmental affiliation of samples reveals a strong facies shift across the sequence boundary. Ordination methods show that benthic assemblages of the two stages, including 4 biozones and four 3rd order depositional sequences over less than four million years, are developed along the same depth-related environmental gradient. Almost all samples are from highstand systems tracts, but Karpatian faunas are mostly from nearshore settings, and Badenian faunas are strongly dominated by sublittoral assemblages. This study emphasizes the importance of highly resolved stratigraphic and palaeoenvironmental frameworks for deciphering palaeodiversity patterns at regional scales and highlights the effort required to reach the asymptote of the collector's curve. Abundance data facilitate the recognition of ecological changes in regional biota and it is suggested that in second and higher order sequences the facies covered within systems tracts will drive observed diversity patterns.