The microbial communities of the Southern Benguela upwelling region were sampled quarterly through one year, with sampling, taking place in May, September, November and February and spanning the 2015-2016 upwelling season. Community dynamics were assessed at stations both inside and outside a plume of upwelled water. 16S and 18S amplicon results respectively revealed a significant difference in both prokaryote and picoeukaryote communities by season, with a significant difference in community structure between sites during the upwelling season (austral summer) but not in the austral winter samples (non-upwelling). The parasitic dinoflagellate Syndiniales dominated upwelling samples, and diatoms (Mediophyceae) mostly occurred in the autumn samples. 16S amplicon results revealed a high presence of Nitrosopumillus, an ammonium oxidiser, offshore in February. A significant abundance of Nitrospina sp, a nitrite oxidizer, was found in September hypoxic and deep water samples. Flavobacteriales, SAR11 and Roseobacter sp. dominated the remaining samples. The significant parasitic as well as nitrifying bacterial signals have far reaching implications with regard to biogeochemical cycling in this region.