Marine heatwaves are defined by periods of unusually high sea temperature. Although warmer seawater usually reduces the ocean’s ability to absorb carbon dioxide, observations in the Gulf of Alaska showed a surprising drop in carbon dioxide during the 2014–2015 “Blob” heatwave. Using an ocean biogeochemical model, we found that this decline resulted from reduced dissolved inorganic carbon caused by weakened physical supply in winter 2013, just before the Blob began.