River plume‐impacted shelf marginal seas exhibit strong carbon sequestration potential due to their high biological productivity. However, frequent coastal upwelling events complicate the carbon source‐sink dynamics because of the competing effects on seawater partial pressure of carbon dioxide (pCO2): the upwelling of dissolved inorganic carbon (DIC)‐rich deep waters initially elevate surface pCO2, while subsequent biological uptake lowers it. As a case study, we used a novel wave‐driven profiler to obtain high‐resolution vertical profiles in the Changjiang plume‐impacted shelf area (CPS) and to investigate upwelling‐induced variability in pCO2 and carbon source‐sink dynamics. The observations were conducted near Gouqi Island, where coastal upwelling frequently occurs. Based on a pCO2 mass balance model, we found that biological processes (contributing 30.6% to pCO2 increase) and physical transport (contributing 21.2% to pCO2 decrease) jointly dominated hourly mixed layer pCO2 variability in the study area. Importantly, we found that αSBW (shelf bottom water fraction) served as a good quantitative proxy for upwelling intensity, with each 1% increase in αSBW associated with a 6‐μatm increase in mixed layer.Given the significantly higher mean αSBW values during 20–22 August (34 ± 5%) than 28–30 August (11 ± 7%), we defined the former as the upwelling period and the latter as the post‐upwelling period. The air‐sea CO2 flux (FCO2) during the upwelling period (24.04 ± 16.24 mmol m