Two contrasting high nutrient/low chlorophyll regions having different conditions that control phytoplankton production, and separated by an area of blooming, are found during summer in the vicinity of the South Shetland Islands (Antarctica). Low chlorophyll conditions occur either in Fe-rich, deeply mixed and high salinity Weddell Sea shelf waters, or the Fe-poor, shoaled and low salinity Drake Passage Antarctic Circumpolar Current waters, while phytoplankton blooms are located between in mid salinity water. Contrasting phytoplankton communities were found to populate these different biogeochemical provinces. In data from six field seasons (1999–2007), nanoplankton (2–20 μm) were found to be dominant in the phytoplankton populations from light-controlled coastal waters, including blooms, with most chlorophyll found in the 2–5 μm size class. In contrast, the adjacent and presumably Fe-controlled Drake Passage waters were dominated by the microplankton (> 20 μm) size class. The asymmetrical distribution of phytoplankton size classes across the salinity gradient, when analysed independently of total chlorophyll concentration, supports the hypothesis that the different food web grazing dynamics are dependent upon biogeochemical provinces.