Rapid climate warming and sea-ice loss have induced major changes in the sea surface partial pressure of CO2 (pCO2). However, the long-term trends in the western Arctic Ocean are unknown. Here we show that in 1994–2017, summer pCO2 in the Canada Basin increased at twice the rate of atmospheric increase. Warming and ice loss in the basin have strengthened the pCO2 seasonal amplitude, resulting in the rapid decadal increase. Consequently, the summer air–sea CO2 gradient has reduced rapidly, and may become near zero within two decades. In contrast, there was no significant pCO2 increase on the Chukchi Shelf, where strong and increasing biological uptake has held pCO2 low, and thus the CO2 sink has increased and may increase further due to the atmospheric CO2 increase. Our findings elucidate the contrasting physical and biological drivers controlling sea surface pCO2 variations and trends in response to climate change in the Arctic Ocean.