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Abstract Seasonal variations in the transports of total alkalinity (TAlk) and dissolved inorganic carbon (DIC) from the Lower Changjiang (Yangtze) River/Estuary to the East China Sea were investigated based on a series of field surveys in 2015–2017, including monthly samplings at Datong Station and seasonal mapping cruises in the Changjiang Estuary and the adjacent northwestern East China Sea. In comparison with historical data sets, the Changjiang TAlk flux varied around a nearly stable average over the past 55 years. This is much different from some American rivers, where TAlk export fluxes increased for a century long. To assess effects of riverine carbonate inputs on coastal carbonate chemistry, we compared several cases showing freshwater‐dilution‐induced decline in coastal aragonite saturation state (Ωarag), including rainwater dilution and riverine water dilution. Without riverine carbonate inputs, the effect of a unit of salinity decrease (due to rainwater dilution) on Ωarag was expected to be counteracted by a DIC removal of 10 μmol/kg relative to the baseline value along relevant conservative mixing line, when coastal Ωarag was close to a critical value of 1.5. Considering terrestrial carbonate inputs from Changjiang, however, the freshwater‐dilution‐induced coastal Ωarag suppression decreased by 12%. Our data also showed that more than 10% of wet‐season DIC flux discharged from the Changjiang Estuary was sequestered by biological activities in nearshore areas, while the TAlk flux was rarely affected. This biological alteration effectively transformed the terrestrial carbonate system from a feature of DIC:TAlk >1.0 to the usual seawater feature of DIC:TAlk