Abstract Acidification and hypoxia present significant ecological and environmental challenges for coastal oceans, particularly estuarine systems with high nutrient inputs such as the Changjiang Estuary (CJE). We conducted three replicate cruises from July to September in 2020 along the same transects off the CJE to investigate dynamic changes of coastal acidification and hypoxia. Bottom hypoxia expanded and intensified from July to August and alleviated in September. Changes in pH T generally followed those of dissolved oxygen (DO), although the spatial and temporal patterns did not entirely align. In August, the tight connection between hypoxia and acidification differed between the northern and southern regions. The northern region experienced widespread hypoxia and acidification with DO and pH T as low as 39 μmol kg −1 and 7.66, whereas the southern region maintained similar pH T values despite higher DO (>94 μmol kg −1 ). By September, hypoxia was alleviated, and pH T showed a more pronounced rise, with pH T increasing by ∼0.02 at the same DO level. Aerobic remineralization emerged as the primary driver of bottom acidification and hypoxia off the CJE during summer, peaking in August and diminishing by September. In August, the northern region experienced synchronous and severe hypoxia and acidification, whereas intermittent localized mixing in the south alleviated hypoxia. By September, enhanced mixing in the CJE increased the buffering capacity of subsurface waters, mitigating pH decline despite ongoing hypoxia. These findings improve our understanding of short‐term dynamics in estuarine carbon cycling, acidification and hypoxia.