The rapid warming of the West Antarctic Peninsula region has led to reduced sea ice cover and enhanced glacial melt water input. This has potential implications for marine ecosystems, notably phytoplankton growth, biomass, and composition. Fifteen years (1997–2012) of year-round size fractionated chlorophyll a (Chl a), phytoplankton pigment fingerprinting and environmental data were analyzed to identify the relationship between sea ice cover, water column stability and phytoplankton dynamics in northern Marguerite Bay, Antarctica. Over the investigated period, both summer (December–February) and winter biomass declined significantly, 38.5% and 33.3% respectively. Winter phytoplankton biomass was low ( 20 μm) fraction was strongly decreased in the low biomass years, from 92% to 39%, coinciding with a smaller diatom fraction in favor of nanophytoplankton ( 95%) during summers with average-to-high biomass. We advance a conceptual model whereby low winter sea ice cover leads to low phytoplankton biomass and enhanced proportions of nanophytoplankton, when this coincides with reduced stratification during summer. These changes are likely to have a strong effect on the entire Antarctic marine food web, including krill biomass, and distribution.