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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 (< 0.25 μg Chl a L⁻¹) and consisted on average of 69% diatoms, 5% cryptophytes, and 20% haptophytes. Summers following winters with low (< 65 days) sea ice cover were characterized by …