The Kerguelen Plateau is a region of natural iron fertilization in the Southern Ocean, within the typically iron limited High Nutrient Low Chlorophyll (HNLC) waters of the eastward flowing Antarctic Circumpolar Current. Between 26 February and 19 March 2018, the MOBYDICK expedition investigated pelagic ecosystem dynamics in the Kerguelen Island region on the northern plateau during the post-phytoplankton bloom period. The survey specifically targeted sampling at two stations in the HNLC waters to the west of the Kerguelen Plateau, and in the iron enriched waters on and to the east of the plateau. A combination of WP2, WP3 and Mesopelagos midwater trawl were used to sample the mesozooplankton (125 μm to ≤ 10 mm), macrozooplankton (10–30 mm) and micronekton (> 30 to 200 mm) communities. Stable carbon (δ¹³C) and nitrogen (δ¹⁵N) isotopes were measured across representative samples of taxa from all stations. Trophic positions was estimated using a Bayesian isotope mixing model (tRophicPosition), that uses both the δ¹³C and δ¹⁵N values of baselines and consumers. Meso/macrozooplankton trophic positions (TPs) were ~ 2.4 on the plateau and > 0.6 TPs higher at the upstream HNLC stations. This provides empirical evidence for shorter food chains on the diatom dominated plateau and longer food chains in the HNLC region dominated by pico and nanophytopklankon. Meso/macrozooplankton TPs were also elevated downstream of the plateau, though to a lesser extent than in the upstream region, likely reflecting the effect of downstream iron transport, supporting elevated phytoplankton production in the downstream region. There was a consistent increase in trophic position between meso/macrozooplankton and micronekton of ~ 0.6 at all stations. Food chain length was therefore determined by the composition of and interactions between the trophic levels below micronekton. Similar trophic structure at the two upstream HNLC stations, on either side of the northern branch of the Polar Front, indicated that food chain length was robust to the differences in community composition, and supports the critical role of size structured trophic interactions in determining food web properties.