We analysed field-collected quantitative data of benthic marine molluscs across the Cretaceous–Palaeogene boundary in Patagonia to identify patterns and processes of biodiversity reconstruction after the end-Cretaceous mass extinction. We contrast diversity dynamics from nearshore environments with those from offshore environments. In both settings, Early Palaeogene (Danian) assemblages are strongly dominated by surviving lineages, many of which changed their relative abundance from being rare before the extinction event to becoming the new dominant forms. Only a few of the species in the Danian assemblages were newly evolved. In offshore environments, however, two newly evolved Danian bivalve species attained ecological dominance by replacing two ecologically equivalent species that disappeared at the end of the Cretaceous. In both settings, the total number of Danian genera at a locality remained below the total number of late Cretaceous (Maastrichtian) genera at that locality. We suggest that biotic interactions, in particular incumbency effects, suppressed post-extinction diversity and prevented the compensation of diversity loss by originating and invading taxa. Contrary to the total number of genera at localities, diversity at the level of individual fossiliferous horizons before and after the boundary is indistinguishable in offshore environments. This indicates an evolutionary rapid rebound to pre-extinction values within less than ca 0.5 million years. In nearshore environments, by contrast, diversity of fossiliferous horizons was reduced in the Danian, and this lowered diversity lasted for the entire studied post-extinction interval. In this heterogeneous environment, low connectivity among populations may have retarded the recolonisation of nearshore habitats by survivors.