Subsurface accumulations of chlorophyll, also known as deep chlorophyll maxima (DCMs), have been studied in the tropical and temperate oceans for decades, but they have received less attention in the Southern Ocean. Their formation and maintenance are still under debate, as is their contribution to phytoplankton biomass and net primary productivity (NPP). Recently, the application of satellite-based NPP algorithms to data from biogeochemical (BGC)-Argo floats has improved vertically-resolved NPP estimates. Using this new approach on 247 BGC-Argo floats, we report (1) subsurface (below the mixed layer) estimates of NPP, (2) the contribution of subsurface NPP to total NPP, and (3) the influence of DCMs and deep biomass maxima (DBMs, based on particulate backscatter) on (1) and (2). We compare and contrast trends in adjacent latitudinal bands in the southern hemisphere, south of 30°S, from nitrate-limited oligotrophic waters to iron-limited high-nutrient, low-chlorophyll (HNLC) regions. This comparison of pervasive DCMs in oligotrophic waters with the same features in HNLC waters reveals differences in seasonality of DCM occurrence and their contribution to total NPP. Unlike oligotrophic DCMs, HNLC DCMs occur only during spring and summer, and their contribution to total NPP decreases from ~40% to ~25% through the productive season, likely linked to the availability of iron and silicate. When DCMs are present but not accounted for, up to 45% of NPP is not quantified. Our results highlight the importance of understanding the vertical structure of phytoplankton stocks and productivity, with direct impacts on global NPP estimates and, ultimately, the biological carbon pump.