We describe the invertebrate assemblages in the Middle Jurassic to lowermost Cretaceous of the Agardhfjellet Formation present in the DH2 rock-core material of Central Spitsbergen (Svalbard). Previous studies of the Agardhfjellet Formation do not accurately reflect the distribution of invertebrates throughout the unit as they were limited to sampling discontinuous intervals at outcrop. The rock-core material shows the benthic bivalve fauna to reflect dysoxic, but not anoxic environments for the Oxfordian–Lower Kimmeridgian interval with sporadic monospecific assemblages of epifaunal bivalves, and more favourable conditions in the Volgian, with major increases in abundance and diversity of Hartwellia sp. assemblages. Overall, the new information from cores shows that abundance, diversity and stratigraphic continuity of the fossil record in the Upper Jurassic of Spitsbergen are considerably higher than indicated in outcrop studies. The inferred life positions and feeding habits of the benthic fauna refine our understanding of the depositional environments of the Agardhfjellet Formation. The pattern of occurrence of the bivalve genera is correlated with published studies of Arctic localities in East Greenland and northern Siberia and shows similarities in palaeoecology with the former but not the latter. Ammonite biostratigraphy is used as a tool to date bivalve assemblage overturning events to help identify similar changes in other sections.