Abstract The diverse and productive blue carbon ecosystems (mangrove, seagrass, salt marsh, and macroalgae) provide many ecosystem services and play an important role in climate change mitigation and adaptation. However, less is known about how different biogeochemical processes within blue carbon ecosystems can influence seawater carbonate dynamics especially on the partial pressure of carbon dioxide ( p CO 2 ) and pH. Through underway p CO 2 measurements and discrete water samples, we examined the spatial and temporal distributions of the carbonate system in two tropical mangrove estuaries and one benthic‐macroalgae‐vegetated lagoon. In early summer, the mangrove estuaries behaved as weak CO 2 sources of 2.0–4.0 mmol m −2 d −1 , whereas the tropical lagoon became a CO 2 sink of −6.4 mmol m −2 d −1 . The chemical stoichiometry, stable carbon isotope, and other geochemical tracers reveal that carbonate dissolution and sulfate reduction followed by aerobic respiration are dominant controls on carbonate dynamics in mangrove estuaries. Without alkalinity enhancement driven by carbonate dissolution and sulfate reduction mainly from mangrove sediments, CO 2 emission would be 23 times larger than current observation, and pH would decrease by 0.39 units on an estuary‐wide scale. However, in macroalgae‐inhabited lagoon primary production followed by carbonate formation could draw p CO 2 down to 70 μatm and raise pH to 8.8, which are significantly distinct from the normal estuarine water. This study demonstrates that lateral export of alkalinity from mangrove sediments and the in situ metabolism of macroalgae can significantly influence the estuarine air‐sea CO 2 flux and acidification status, and emphasizes the importance of protecting and restoring the blue carbon ecosystems.