Analysis of benthic foraminifera in surface samples from 23 sites on the Northeast Greenland continental shelf reveal key assemblage differences between sites. Cluster analysis creates two clear geographical faunal assemblage zones: the 1) inner shelf, and 2) mid and outer shelf sites. These assemblages differ significantly, with the inner shelf sites being characterised by a high percentage and concentration of calcareous species, whilst the mid and outer shelf sites are dominated by agglutinated taxa. At almost all sites, the calcareous assemblages are dominated by Cassidulina neoteretis and Cassidulina reniforme, suggesting that they thrive across the shelf. Stetsonia horvathi, Oridorsalis tener, as well as Glomulina oculus and other miliolid species are found to be key calcareous species at many sites in the inner shelf zone, but they are rare-to-absent on the mid and outer shelf. Canonical correspondence analysis shows that September sea-ice cover and bottom water oxygen content are positively correlated with benthic foraminiferal assemblages at inner shelf sites, whereas organic carbon content is correlated with those in the mid and outer shelf. The formation of seasonal sea-ice and the Northeast Water polynya rejects brine into surrounding waters and transports CO2 to the seafloor, creating a highly corrosive environment for calcium carbonate. These environments are also highly productive, as indicated by the high organic carbon content and low bottom water oxygen content. The oxidation of this organic material creates CO2. We propose that these processes are key drivers in the dissolution of calcareous tests. In contrast, extensive sea-ice, high bottom water oxygen content and low primary productivity in the glacier-proximal region facilitates carbonate preservation.