The carbon and nitrogen isotope ratios (δ13C and δ15N) of marine plankton record biogeochemical processes at the base of the food web. In the Southern Ocean, such data, predominantly from summer, have been used to infer surface CO2 concentrations and the potential for biological carbon export. However, variability in plankton δ13C and δ15N remains poorly understood, with the lack of seasonal measurements from the Southern Ocean emerging as a particular limitation. Here, we investigate the δ13C and δ15N of suspended particulate matter (SPM) and zooplankton collected from the Subantarctic Ocean in winter, summer, and autumn. The low summertime δ13CSPM and δ15NSPM can be explained by strong diatom reliance on nitrate supplied during winter mixing. A subsequent increase in δ13CSPM and decrease in δ15NSPM by autumn is consistent with iron limitation in mid‐ to late‐summer favoring diatom succession by nano‐phytoplankton that consume mainly recycled ammonium. By winter, bacterial decomposition of biomass outpaces new biomass production, decreasing δ13CSPM and raising δ15NSPM. The δ13C and δ15N of contemporaneously sampled zooplankton generally reflect the variability in δ13CSPM and δ15NSPM, with one autumn mismatch suggesting that in situ SPM is not always the dominant zooplankton food source. Our study shows how nutrient dynamics and phytoplankton community composition shape the seasonality of the Subantarctic's isotopic baselines, emphasizing a key role for iron availability. This work has implications for isotope‐based food web studies, highlighting the need to consider seasonal variability in δ13CSPM and δ15NSPM, as well as the different turnover times of phytoplankton (i.e., SPM) vs. zooplankton biomass.