Surveys of the microplankton communities of the Scotia Sea, Southern Ocean, were carried out during three separate seasons of interest, spring, summer, and autumn of consecutive years. The surveys were conducted along a south to north transect and covered areas of low and high productivity, as well as crossing deep, open water and shallow, bathymetric features. During the summer and autumn cruises, cluster analysis revealed four distinct communities that were broadly consistent between cruises. From south to north the zones in which the communities fell were as follows: SOUTH, stations in the south Scotia Sea; MID, stations in the central Scotia Sea; SW-SG, stations southwest of the island of South Georgia; and NW-SG, stations northwest of South Georgia. Two main groups dominated the microplankton communities in all zones and all seasons; diatoms and naked, heterotrophic dinoflagellates. However, the proportion of these groups, and the species of diatom present, varied between zones and between seasons. In the SOUTH zone, a cryptophyte bloom was observed during summer. Spring and autumn communities showed similar levels of Chl a (0.6–1.5 mg m−3) but shifted to increasing numbers and biomass of heavily silicified diatoms (Fragilariopsis spp. and Corethron pennatum). Dense, spring blooms of the MID zone were dominated by a weakly silicified diatom, Thalassiosira spp. This contrasted with production 10 times lower (∼0.2 g C m−2 d−1) during the dinoflagellate composed, summer and autumn cruises. Closer to the island of South Georgia, lightly silicified diatoms became increasingly prevalent. In the SW-SG zone, such diatoms were found both in low Chl a (0.3 mg m−3) spring-time waters and in short-lived summer blooms. Autumn communities saw a switch to dinoflagellates co-inciding with decreasing light levels and depletion of macronutrients. Downstream of South Georgia, in the NW-SG zone, high productivity (up to 2.8 g C m−2 d−1) and long lasting blooms (3–6 months) were found on all seasons surveyed. The NW-SG microplankton consisted of a mixed community with both heavily and weakly silicified diatoms, but also significant amounts of heterotrophic dinoflagellates. Using bloom dynamics, microplankton structure and diatom speciation of our 4 Scotia Sea zones, we propose the following potential export regimes: (1) SOUTH – weak export of carbon, (2) MID – episodic, dense pulses of carbon may be exported, (3) SW-SG – modest pulses of carbon may be exported, and (4) NW-SG – high export of biogenic carbon likely to occur.