In ice-covered areas in the Arctic, production by ice algae can be the main input of organic matter to the ecosystem. Pelagic–benthic coupling is thought to be particularly tight in those areas. The increase of ice algal production in Franklin Bay from January/February to April/May 2004 was found to be accompanied by an increase in sediment oxygen demand (SOD; Renaud and others, 2007). However sedimentary chlorophyll a, which is usually an indicator of inputs of ‘fresh’ organic matter to the sea floor, did not increase. Consequently, it was asked what was the fate of ice algal phytodetritus arriving at the sea floor? In order to answer that question, photosynthetic pigments from the sea ice, particulate organic matter, and sediment, and diatom frustules in the sediment, were studied from January to May 2004. Ice algal diatom cells in the sediment showed an increase in April/May, confirming the higher inputs of fresh ice algae to the sediment. Changes in sedimentary pigment profiles in the first 10 cm suggested an increase in sediment reworking due to the enhanced benthic activities. Finally, changes in phaeopigments composition and increase of total SOD vs microfauna SOD implied an increase in macrobenthic activities. Benthic macrofauna consumed some of the deposited material and mixed some within the top 5 cm of sediment. The response of sedimentary pigments to an ice algae input can be studied at different levels and it is the combination of these studies that allows understanding of the overall fate of phytodetritus in the benthic compartment.