Coastal ecosystems connect terrestrial and marine carbon cycles, yet the understanding of how blue carbon plants influence the estuarine carbon transport and transformation remains insufficient. Here we conducted eight field surveys on the carbonate system in a tropical lagoon in the northern Hainan Island, China from June 2022 to February 2024. We estimated the riverine export of dissolved inorganic carbon, and the air-sea CO₂ flux within the lagoon. The distributions of carbonate system exhibit significant seasonal patterns with a strong CO₂ uptake in the southern region, and weak to moderate CO₂ sources in the northern lagoon. A two-endmember mixing model was applied to compute the nonconservative concentrations of DIC, TA and Ca²⁺, which were used to infer the underlying dominant biogeochemical processes. Annual DIC exports from individual rivers ranged from 0.125 to 0.183 × 10⁹ mol yr⁻¹, with a catchment-area-normalized DIC flux of 1.205 × 10⁶ mol km⁻² yr⁻¹. Xiaohai Lagoon showed pronounced seasonal shift on CO₂ source/sink patterns, with the highest mean emission in April 2023 (19.1 ± 27.4 mmol m⁻² d⁻¹) and the strongest uptake in November 2023 (−26.9 ± 11.9 mmol m⁻² d⁻¹). The annual mean air–sea CO₂ flux was −1.15 mol m⁻² yr⁻¹, indicating an overall weak CO₂ sink. Non-conservative removal of DIC, TA and Ca²⁺ in the southern lagoon coincided with high DO, high pH and low pCO₂, consistent with the combined effects of net autotrophy and carbonate precipitation or biological calcification. Water-column net community production evaluated by the classic light–dark incubations varied substantially in space and time and could not fully explain the persistent carbonate anomalies in the southern region. Their spatial and seasonal distributions well correlated with benthic plants coverage and its growth cycles suggesting that benthic plants may be important regulators of CO₂ uptake and acidification buffering in Xiaohai Lagoon. Our study may shed light on the estuarine carbonate dynamics responding to the ongoing/future recovery of benthic plants that serves as one of the nature-based solutions for climate change mitigation and adaption.

Keywords: tropical lagoon; riverine inorganic carbon flux; air–sea CO₂ flux; carbonate system; benthic plants