The food web structure and diets of 26 taxa of benthic boundary layer (BBL) zooplankton on the Beaufort Sea shelf were studied using carbon and nitrogen stable isotopes and fatty acids. Mean delta N-15 values ranged from 7.3 parts per thousand for the amphipod Melita formosa to 14.9 parts per thousand for an unidentified polychaete, suggesting that taxa sampled came from three trophic levels. For 8 taxa, the lightest carbon signature occurred near the mouth of the Mackenzie River. Stable isotope ratios helped clarify the origin of signature fatty acids. Levels of certain polyunsaturated fatty acids (PUFA) were negatively correlated with delta N-15, with the exception of 22:6 omega 0, which was positively correlated with delta N-15, suggesting that this essential PUFA was retained through the food web. Discriminant analysis proved to be a powerful tool, predicting taxa from fatty acid profiles with 99% accuracy, and revealing strong phylogenetic trends in fatty acid profiles. The amphipod Arrhis phyllonyx had higher levels of omega 6 PUFA, especially 20:4 omega 6 with several possible sources, than other peracarid crustaceans. The holothurian had high levels of odd numbered and branched chain fatty acids, indicative of bacterial consumption, while fatty acids of phytoplankton origin were important discriminants for Calanus hyperboreus and the chaetognaths Eukrohnia hamata and Parasagitta elegans. This relationship indicates that the conventional phytoplankton-copepod-chaetognath food web found in the water column also exists in the BBL. This observation, as well as generally low delta N-15 and high levels of certain PUFA in samples with lower delta N-15, strongly suggests that BBL zooplankton on the Beaufort Sea shelf have access to fresh material of phytoplankton origin either by feeding on sedimenting matter or by active migration to surface waters. (C) 2013 Elsevier Ltd. All rights reserved.