The global ocean is an important sink for anthropogenic CO2 (ref. 1). Nearly half of the oceanic CO2 uptake occurs in the Southern Ocean2. Although the role of the Southern Ocean CO2 sink in the global carbon cycle is recognized, there are uncertainties regarding its contemporary trend3,4, with a need for improved mechanistic understanding, especially in productive Antarctic coastal regions experiencing substantial changes in temperature and sea ice5. Here, we demonstrate strong coupling between summer upper ocean stability, phytoplankton dynamics and oceanic CO2 uptake along the rapidly changing West Antarctic Peninsula using a 25-year dataset (1993–2017). Greater upper ocean stability drives enhanced biological production and biological dissolved inorganic carbon drawdown, resulting in greater oceanic CO2 uptake. Diatoms achieve higher biomass, oceanic CO2 uptake and uptake efficiency than other phytoplankton. Over the past 25 years, changes in sea ice dynamics have driven an increase in upper ocean stability, phytoplankton biomass and biological dissolved inorganic carbon drawdown, resulting in a nearly fivefold increase in summer oceanic CO2 uptake. We hypothesize that continued warming and declines in sea ice will lead to a decrease in biological dissolved inorganic carbon drawdown, negatively impacting summer oceanic CO2 uptake. These results from the West Antarctic Peninsula provide a framework to understand how oceanic CO2 uptake in other Antarctic coastal regions may be altered due to climate change.