Body size, depth of occurrence, and local oceanography shape trophic structure in a diverse deep-pelagic micronekton assemblage

•Estimations of trophic structure using stable isotopes identified fewer trophic groupings than estimations using diet data.•Body size, depth of occurrence, and proximity to an oceanographic feature were important drivers of isotopic variability.•Body size (migrators) and nighttime depth (non-migrators) were the most important factors explaining isotopic variation.•High δ15N values in non-migrators at deeper depths suggests these species use food webs with isotopically enriched baselines.•The use of elevated isotopic baselines in some species is important as it can lead to overestimation of trophic position.