Nitrogen availability in the open ocean regulates primary productivity and a cascade of associated carbon-nitrogen coupled transformations mediated by both eukaryotic and prokaryotic microorganisms. An understanding of potential alterations at the base of the food chain particularly reductions in planktonic biomass is essential, as a decline or community shift in primary productivity will impact ecosystem services, such as O2 production, carbon sequestration and biogeochemical cycling. This study, as part of the OISO (Ocean Indien Service d'Observation) campaign, aimed to shed light into prokaryotic and photoautotrophic, eukaryotic community composition between four different water masses as well carbon and nitrogen assimilation rates in the Southern Indian Ocean and the French Southern and Antarctic lands. To understand ecosystem dynamics, we linked microbial community composition, using high resolution molecular 16S rDNA amplicon sequencing techniques and functional pigment analysis, to in situ rate measurements of carbon (C) and nitrogen (N). While temperature and salinity were the driving factors for carbon fixation, water masses defined prokaryotic community composition. We could link prokaryotic diversity to high carbon fixation rates emphasizing positive foodweb recoupling and recycling processes. Photoautotrophic community composition clearly separated between the warm Indian Ocean and the Southern Ocean. While the Indian Ocean was vastly dominated by the unicellular cyanobacterium Prochlorococcus, the relative abundance of the diatom diagnostic pigment fucoxanthin increased in the Southern Ocean. C fixation was relatively higher (84.8 ± 44.5 μmol L-1 h-1) in the nutrient-rich Southern Ocean, in comparison to the oligotrophic Indian Ocean (14.2 ± 7.9 μmol L-1 h-1). In general, high variations within-station replicates of C fixation were found, ranging from 43.4 – 134.9 μmol L-1 h-1. We measured N2 fixation at all sampling stations, up to 56°S latitude, supporting the hypothesis that N2 fixation is an ubiquitous process which is not restricted to warm oligotrophic water. N2 fixation rates showed similar patterns as C fixation rates within station replicates, ranging from 0.9 to 7.9 nmol N L-1 d-1. Among other interpretations, this suggests sub-mesoscale dynamics and potential small-scale differences in biochemical conditions. Our observations point out the importance of high resolution (i.e., sub-mesoscale and smaller) in situ studies in combination with remote- sensing techniques, to be able to fully understand the scale of variation in ocean dynamics. ii Collectively our results are another piece of the puzzle of the complex dynamics in the Southern Indian Ocean sector. Understanding biogeochemical and biological processes supports our ability to further understand C and N fluxes to be able to predict and model future climate change scenarios.