The composition of particles obtained by annually moored sediment traps have been analysed at the Long-Term Ecological Research (LTER) site HAUSGARTEN in Fram Strait (79°/4°E) since 2000. The open ocean observatory is seasonally covered by sea ice and is influenced by the inflow of relatively warm Atlantic Waters at the surface. Exceptionally warm Atlantic Water with temperatures of >3°C entered Fram Strait during 2006/7. We present data on the export of total particulate matter (TPM), particulate organic carbon and nitrogen (POC/PON), biogenic particulate silica (bPSi), calcium carbonate (CaCO3), and protist composition achieved during 2000-2011. Annual fluxes showed greatest variation (3-5 folds) for TPM and CaCO3 flux and a drastic decrease in bPSi, a proxy for diatoms, after 2004. Variations in the flux of CaCO3 and its increase during and after the warming event in 2006/7 could be attributed to an increase of pteropods, namely the boreal species Limacina retroversa. Pteropod carbonate (aragonite) dominated with up to ~80% in the total CaCO3 flux, which is also reflected in the POC/PIC ratio indicating repercussions on the biological carbon pump.