Polar marine ecosystems are particularly vulnerable to the effects of climate change. Warming temperatures, freshening seawater and disruption to sea ice formation potentially all have detrimental cascading effects on food webs. New approaches are needed to better understand spatio-temporal interactions among biogeochemical processes at the base of Southern Ocean food webs, and how these interactions vary seasonally. In marine systems, isoscapes (models of the spatial variation in the stable isotopic composition) of carbon and nitrogen identify the spatial expression of varying biogeochemical processes on nutrient utilization by phytoplankton. Isoscapes also provide a baseline for interpreting stable isotope compositions of higher trophic level animals in movement, migration and diet research. Here we produce carbon and nitrogen isoscapes across the entire Southern Ocean (>40°S) using surface particulate organic matter (POM) isotope data, collected from multiple sources over the past 50 years and throughout the annual cycle. We use Integrated Nested Laplace Approximation (INLA)-based approaches to predict mean annual isoscapes and four seasonal isoscapes using a suite of environmental data as predictor variables. Clear spatial gradients in δ13C and δ15N values were predicted across the Southern Ocean, consistent with previous statistical and mechanistic isoscape views of isotopic variability in this region. We identify strong seasonal variability in both carbon and nitrogen isoscapes, with key implications for the use of static or annual average isoscape baselines in animal studies attempting to document seasonal migratory or foraging behaviours.