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In the Western Antarctic Peninsula (WAP), marine plankton dynamics are tightly linked to the interannual variability in environmental conditions, including phenological shifts in sea‐ice seasonality. To explore these linkages, we use a 1‐dimensional vertical ocean‐ice‐ecosystem model (KPP‐Eco‐Ice, or KEI) that simulates physical and ecosystem conditions at a continental shelf mooring location in the Palmer Long Term Ecological Research program sampling grid. KEI allows for year‐round examination of the ecosystem in a region where in situ observations on the shelf are limited to January. Comparisons are made between seasonal sea‐ice retreat, mixed layer depth, primary productivity, and phytoplankton relative abundance, grazing, and loss rates. KEI successfully captures seasonal patterns in the WAP, demonstrating that total seasonal primary production was highest following a winter with late sea‐ice retreat. Stability in the surface mixed layer enables high photosynthetic rates by alleviating light limitation, while wind‐induced surface mixing results in lower phytoplankton production and biomass in years with early sea‐ice retreat. However, mixing reduces iron limitation in surface waters, which may influence phytoplankton species composition. Small, non‐diatom phytoplankton are better‐adapted to high light and low iron conditions, thriving longer in a year with late sea‐ice retreat and higher seasonal primary production, while larger diatoms are more abundant in the years with early sea‐ice retreat and lower seasonal production. These findings have implications for grazer populations and subsequent carbon export from the surface to depth in the WAP region. This study validates the role that sea ice plays in shaping Antarctic ecosystem dynamics.