The Chukchi and Beaufort Sea shelves host diverse and productive seafloor ecosystems important for carbon and nitrogen cycling for the Arctic Ocean. The benthic food web transfers energy from primary producers to high trophic level organisms (e.g., birds, fish, and mammals), which are important for cultural practices and subsistence hunting by Native Alaskans. This work focuses on the trophic ecology of arctic food webs through use of several different approaches. First, variation in the natural abundance of stable carbon and nitrogen isotopes facilitated the identification of trophic pathways and, subsequently, allowed the comparison of trophic guilds and food webs from the Chukchi and Beaufort Seas. Compared to water column and sedimentary organic matter end-members, second trophic level grazers and suspension feeders were conspicuously ¹³C-enriched throughout the Chukchi Sea, which supports the hypothesis that microbial degradation of organic matter occurred prior to metazoan assimilation. Second, food web recovery from disturbances caused by exploratory oil drilling at the seafloor that had occurred approximately 20 years prior were assessed in both the Chukchi and Beaufort Seas. Based on isotopic trophic niche overlap between organisms common to drilled and reference sites in the Chukchi and Beaufort Seas, the oil drilling sites had similar food web structure, indicating recovery from the activity associated with the drilling process. Third, photosynthetic pigment biomarkers were used to better understand the diagenetic process, specifically focusing on how both microbial and metazoan grazing pathways degrade organic matter in relation to seasonal sea ice retreat in the Chukchi Sea. The benthic macrofaunal and microbial food web caused rapid degradation of organic matter upon the initial pulse of microalgal food sources to the seafloor. These diagenetic pathways are linked to the ¹³C-enrichment of residual organic matter, which corresponds to the stable isotope values measured in the benthic macrofauna. Lastly, high-precision liquid chromatography and spectrophotometry were compared for estimating sedimentary pigments in the marine environment. Substantial differences in pheopigment (chlorophyll degradation products) concentrations were observed between the two techniques, suggesting the need for revisions to the monochromatic spectrophotometric equation that relates absorbance to pigment concentrations. One pheopigment, pheophorbide, was found to interfere with the accuracy of the spectrophotometric equation and caused the overestimation of pheopigments. / text