• WAP coastal areas are able to sustain massive summer phytoplankton blooms.
• WAP coastal areas may act as strong CO2 and NO3 sinks during summer.
• Water column stability is the main driver of high phytoplankton growth rates.
• Glacier meltwater supplies Fe, allowing phytoplankton to nearly exhaust NO3.
• Future higher glacier melting may facilitate complete localized NO3 consumption.
During January and February 2017 massive phytoplankton blooms (chlorophyll 〉 15 mg m−3) were registered in surface waters within two bays in the Western Antarctic Peninsula (WAP). Reflecting these intense blooms, surface waters exhibited high pH (up to 8.4), low pCO2 (〈 175 µatm) and low nitrate concentrations (down to 1.5 µM). These summer phytoplankton blooms consisted mainly of diatoms and were associated with the presence of shallow, surface freshwater plumes originating from glacier-melt outflow which contributed both to stratification and to iron supply, thus facilitating pronounced nitrate and CO2 drawdown. These findings suggest that with future increases in freshwater discharge around the WAP, phytoplankton blooms in the northern WAP may become more dominated by large cells, resembling the blooms occurring further south along the Peninsula. Fresher surface waters enhanced water column stability in both bays, enabling phytoplankton populations to attain high growth rates. Phytoplankton was observed to double their biomass in 2.3 days, consistent with the high net primary production rates recorded in both bays (1.29–8.83 g C m−2 d−1). Phytoplankton growth rates showed a direct mechanistic relationship with changes in water column stability, suggesting that this is a main driver of primary productivity in near-shore Antarctic coastal ecosystems, which agrees with previous findings. After wind induced mixing, the organic matter produced within both bays did not settle inside them, suggesting that it was laterally advected out of the bays. Thus, we hypothesize that highly productive near-shore bay areas in Antarctica may supply organic matter to oceanic waters.