Climate change at the Western Antarctic Peninsula (WAP) is predicted to cause major changes in phytoplankton community composition, however, detailed seasonal field data remain limited and it is largely unknown how (changes in) environmental factors influence cell size and ecosystem function. Physicochemical drivers of phytoplankton community abundance, taxonomic composition and size class were studied over two productive austral seasons in the coastal waters of the climatically sensitive WAP. Ice type (fast, grease, pack or brash ice) was important in structuring the pre-bloom phytoplankton community as well as cell size of the summer phytoplankton bloom. Maximum biomass accumulation was regulated by light and nutrient availability, which in turn were regulated by wind-driven mixing events. The proportion of larger-sized (> 20 µm) diatoms increased under prolonged summer stratification in combination with frequent and moderate-strength wind-induced mixing. Canonical correspondence analysis showed that relatively high temperature was correlated with nano-sized cryptophytes, whereas prymnesiophytes (Phaeocystis antarctica) increased in association with high irradiance and low salinities. During autumn of Season 1, a large bloom of 4.5-µm-sized diatoms occurred under conditions of seawater temperature > 0 °C and relatively high light and phosphate concentrations. This bloom was followed by a succession of larger nano-sized diatoms (11.4 µm) related to reductions in phosphate and light availability. Our results demonstrate that flow cytometry in combination with chemotaxonomy and size fractionation provides a powerful approach to monitor phytoplankton community dynamics in the rapidly warming Antarctic coastal waters.