The downward flux of carbon from the surface ocean to the seafloor fuels benthic invertebrate biomass and drives carbon sequestration. In polar regions, pelago-benthic carbon coupling is shaped by complex processes influenced by climate change, including glacial retreat, water stratification, and warming. Here we examine three high-latitude coastal systems along the Northeast Greenland coast: Dove Bugt, the Brede–Ardencaple Fjord system, and Kong Oscar Fjord, each differing in bathymetry, glacier influence, and exposure to Atlantic Water at depth. Using short-term sediment-traps, hydrographic profiling, sedimentary carbon analyses, and trait-based macrobenthic community data, we assess how vertical particulate organic carbon (POC) export, sedimentary organic carbon stocks (SOC), and benthic biomass and function are linked across the three coastal systems. We found that vertical POC flux and SOC were highly variable in space and showed no consistent relationship with benthic invertebrate carbon biomass. Our trait analysis of the benthic communities revealed that only a subset of trait strategies, particularly only epifaunal suspension feeders, consistently translated carbon availability into standing biomass. Latent variable modelling, which identifies underlying ecological gradients not explained by measured environmental predictors, revealed an additional axis structuring benthic trait biomass and is most consistent with bathymetric relief and associated horizontal redistribution processes. Thus, with our results showing a temporal decoupling among POC export, SOC, and benthic carbon biomass, we propose that future research investigate lateral transport pathways associated with Atlantic Water intrusion and stratification, alongside benthic production and ecosystem functioning, to better understand carbon processing, retention, and sequestration in Arctic systems.