The air–sea-ice CO2 flux was measured in the ice-covered Saroma-ko, a lagoon on the northeastern coast of Hokkaido, Japan, using a chamber technique. The air–sea-ice CO2 flux ranged from −1.8 to +0.5 mg C m−2 h−1 (where negative values indicate a sink for atmospheric CO2). The partial pressure of CO2 (pCO2) in the brine of sea ice was substantially lower than that of the atmosphere, primarily because of the influence of the under-ice plume from the Saromabetsu river located in the southeastern part of the lagoon. This suggests that the brine had the ability to take up atmospheric CO2 into the sea ice. However, the snow deposited over the sea ice and the superimposed ice that formed from snowmelting and refreezing partially blocked CO2 diffusion, acting as an impermeable medium for CO2 transfer. Our results suggest that the air–sea-ice CO2 flux was dependent not only on the difference in pCO2 between the brine and the overlying air, but also on the status of the ice surface. These results provide the necessary evidence for evaluation of the gas exchange processes in ice-covered seas.