Short-term free-drifting particle interceptor traps were deployed at 28 stations from April to July 1998 in the North Water Polynya (northern Baffin Bay). The amount, composition, and vertical transformation of the organic material sinking out of the euphotic zone were assessed. Clear seasonal sedimentation patterns were apparent throughout the Polynya. Maximum sedimentation occurred during the month of June, at which time high sedimentation of intact diatom cells and empty frustules was observed. In July, abundant resting spores and zooplankton feces were sinking out of the euphotic zone. Vertical transformation of the sinking material, between 50 m and 100 m, revealed a consistent loss of ∼30–35% for particulate organic carbon and nitrogen and a loss of ∼10% for biogenic silica. A temperature model of silica dissolution was used to assess the role of temperature in controlling the low loss of biogenic silica observed in the upper water column. Model results show divergence of modeled rates from in situ loss rates at times when the biosiliceous fraction of the sinking material was high. This indicates that biological factors played a key role in reducing biogenic silica dissolution in the North Water Polynya. Sedimentation of intact cells, abundant resting spores, and feces all contributed to enhance preservation of silica in the sinking material. These results suggest that the North Water Polynya is a sink for biogenic silica and emphasize the significance of biological processes in controlling the silica pump in the marine environment.