The aim of this work was to determine the impact of sympagic (ice-associated) algal primary production on the quality of Arctic filter-feeding bivalves. For this purpose, we investigated the sea ice production of lipids (including omega−3 polyunsaturated fatty acids (n-3 PUFA) and highly branched isoprenoids (HBI)), as well as their subsequent incorporation into the truncate softshell clam (Mya truncata) and the Greenland cockle (Serripes groenlandicus) during the melting periods of two consecutive years in Baffin Bay. Lipid and primary production exhibited seasonal variability and overall contrasts between the two years as a result of distinct physical forcings and the ensuing biological responses. Whilst less productive in terms of total lipids or chlorophyll a, Spring 2016 was more productive than Spring 2015 for n-3 PUFA, which are essential for benthic fauna. The sea ice diatom HBI biomarker IP25 was quantified in sea ice from both years. Interestingly, such production was preceded by a production of the hitherto ‘pelagic’ biomarker, HBI III, in sea ice. In bivalves, HBI contents and correlations confirmed the tightness of the Arctic sympagic-benthic coupling and highlighted that S. groenlandicus can be used as a sentinel species for assessing the degree of this coupling. The confirmation that bivalves incorporate sea-ice derived HBI III and not only IP25, may introduce uncertainties into the use of some HBI-based indices. Monitoring of the fatty acid contents of bivalves allowed identification of their spawning periods and suggests that M. truncata did not store enough n-3 PUFA to sustain its reproductive effort.