Zooplankton plays a key role in the marine food webs, and it represents the main food source for small pelagics, one of the most exploited resources in the Adriatic Sea. In order to deepen our knowledge of zooplankton assemblage structure and trophodynamics in one of the most productive areas of the Mediterranean sea, but at the same time highly impacted by human activities, community and Stable Isotope Analyses (SIA) were performed on zooplankton samples. Here SIA data are provided. Zooplankton samples were collected on board R/V G. Dallaporta during the acoustic survey MEDIAS 2019 geographic subarea (GSA) 17 and GSA 18 (Leonori et al., 2021, https://doi.org/10.12681/mms.26001) that took place in June–July 2019, in the continental shelf waters of the western Adriatic Sea. Vertical hauls were performed using a WP2 plankton net, starting from 3 m above the bottom (or from 100 m depth in the deepest hauls), to the surface. Zooplankton samples were frozen on board and analysed in the laboratory to characterize the planktonic community, both at assemblage and trophic structure levels. After taxonomical identification, samples were dried and analysed through an elemental analyser (Thermo FlashEA 1112) for the determination of total carbon and nitrogen and then analysed for δ13C and δ15N in a continuous-flow isotope-ratio mass spectrometer (Thermo Delta Plus XP) (Post et al., 2007, https://doi.org/10.1007/s00442-006-0630-x).

Functional groups (abbreviation: full name: ecological meaning): FF-HERB: filter feeders-herbivores: primary consumers OMN-HERB: omnivores-herbivores: omnivores with a clear tendency toward herbivory, encompassing mostly herbivore species, but that can feed also small particles and ciliates hyperiid Lycaea pulex OMN-CARN: omnivores-carnivores: small carnivores, similarly to OMN-HERB but with greater preference for small zooplankton CARN: carnivores: strictly carnivore species, including also the parasite Lycaea pulex--------------------------------------------------Samples were analyzed through an elemental analyser (Thermo FlashEA 1112) for the determination of total carbon and nitrogen and then analysed for δ13C and δ15N in a continuous-flow isotope-ratio mass spectrometer (Thermo Delta Plus XP) at the Stable Isotope Ecology Laboratory of the University of Palermo (Italy). The stable isotope ratio was expressed, in relation to international standards (atmospheric N2 and Pee Dee Belemnite for δ15N and δ13C, respectively), where R is δ13C or δ15N: (R_sample/R_standard)-1)*10e3. Analytical precision based on standard deviations of internal standards (International Atomic Energy Agency IAEA-CH-6, IAEA-NO-3, and IAEA-N-2) ranged from 0.10 ‰ to 0.19 ‰ for δ13C and 0.02 ‰ to 0.08 ‰ for δ15N.