Global warming causes dramatic environmental change to Arctic ecosystems. While pelagic primary production is initiated earlier and its intensity can be increased due to earlier ice melt and extended open‐water periods, sea‐ice primary production is progressively confined on a spatio‐temporal scale, leading to unknown consequences for the ice‐associated (sympagic) food web. Understanding ecological responses to changes in the availability and composition of pelagic and sympagic food sources is crucial to determine potential changes of food‐web structure and functioning in Arctic marine communities under increasingly ice‐free conditions. Focus was placed on the importance of suspended particulate organic matter vs. sympagic organic matter for 12 zooplankton species with different feeding modes covering five taxonomic groups (copepods, krill, amphipods, chaetognaths, and appendicularians) at two ice‐covered, but environmentally different, stations in the north‐western Barents Sea in August 2019. Contributions of diatom‐ and flagellate‐associated fatty acids (FAs) to total lipid content and carbon stable isotopic compositions of these FAs were used to discriminate food sources and trace flows of organic matter in marine food webs. Combination of proportional contributions of FA markers with FA isotopic composition indicated that consumers mostly relied, directly (herbivorous species), or indirectly (omnivorous and carnivorous species), on pelagic diatoms and flagellates, independently of environmental conditions at the sampling locations, trophic position, and feeding mode. Differences were nevertheless observed between species. Contrary to other studies demonstrating a high importance of sympagic organic matter for food‐web processes, our results highlight the complexity and variability of trophic structures and dependencies in different Arctic food webs.