Abstract. Model studies suggested that human-induced increase in nutrient load may have stimulated primary production and thus enhanced the CO2 uptake capacity in the coastal ocean. In this study, we investigated the seasonal variations of the surface water's partial pressure of CO2 (pCO2sw) in the highly human-impacted Changjiang–East China Sea system between 2008 and 2011. The seasonality of pCO2sw has large spatial variations, with the largest extreme of 170 ± 75 μatm on the inner shelf near the Changjiang Estuary (from 271 ± 55 μatm in summer to 441 ± 51 μatm in autumn) and the weakest extreme of 53 ± 20 μatm on the outer shelf (from 328 ± 9 μatm in winter to 381 ± 18 μatm in summer). During the summer period, stronger stratification and biological production driven by the eutrophic Changjiang plume results in a very low dissolved inorganic carbon (DIC) in surface waters and a very high DIC in bottom waters of the inner shelf, with the latter returning high DIC to the surface water during the mixed period. Interestingly, a comparison with historical data shows that the average pCO2sw on the inner shelf near the Changjiang Estuary has decreased notably during summer, but has increased during autumn and winter from the 1990s to the 2000s. We suggest that this decadal change is associated with recently increased eutrophication. This would increase both the photosynthetic removal of DIC in surface waters and the respiratory release of DIC in bottom waters during summertime, thereby returning more DIC to the surface during the subsequent mixing seasons and/or episodic extreme weather events (e.g., typhoons). Our finding demonstrates that increasing anthropogenic nutrient delivery from a large river may enhance the sequestration capacity of CO2 in summer but may reduce it in autumn and winter. Consequently, the coastal ocean may not necessarily take up more atmospheric CO2 in response to increasing eutrophication, and the net effect largely depends on the relative timescale of air–sea gas exchange and offshore transport of the shelf water. Finally, the case we report for the Changjiang system may have general ramifications for other eutrophic coastal oceans.