Mangrove, seagrass, and coral habitats often lie adjacent to each other in the tropics and subtropics. Lateral carbon fluxes and their consecutive effects on CO2 dynamics and air-water fluxes along the ecosystem continuum are often overlooked. We measured the partial pressure of CO2 in water and associated biogeochemical parameters with a high temporal resolution and estimated air-water CO2 fluxes along the ecosystem continuum. Their lateral fluxes were estimated by using a biogeochemical mass-balance model. The results showed that the waters surrounding mangrove, seagrass, and coral habitats acted as a strong, moderate, and weak source of atmospheric CO2, respectively. The mangrove zone acted as a net source for TAlk, DIC, and DOC, but as a net sink for POC. The contribution of riverine and mangrove-derived OM was substantially high in mangrove sediment, indicating that net transport of POC towards the coastal sea was suppressed by the sediment trapping function of mangroves. The seagrass zone acted as a net source of all carbon forms and TAlk, whereas the coral zone acted as a net sink of TAlk, DIC, and DOC. The lateral transport of carbon from mangroves and rivers offset atmospheric CO2 uptake in the seagrass zone. DOC degradation might increase DIC, and other biogeochemical processes facilitate the functioning of the coral zone as a DOC sink. However, as a result of DIC uptake by autotrophs, mainly in the coral zone, the whole ecosystem continuum was a net sink of DIC and atmospheric CO2 evasion was lowered. We conclude that lateral transport of riverine and mangrove-derived DIC, TAlk, and DOC affect CO2 dynamics and air-water fluxes in seagrass and coral ecosystems. Thus, studies of lateral carbon fluxes at local and regional scales can improve global carbon budget estimates.

Upwelling enhances pCO₂ levels due to injection of carbon‐rich water to the surface despite the removal of carbon due to increase in primary production supported by enhanced nutrients. It is hypothesized that in the Bay of Bengal, upwelling may decrease pCO₂ due to existence of low saline and pCO₂‐poor waters in the subsurface layer. In order to test this hypothesis, a high‐resolution state‐of‐the‐art ocean biogeochemical model (Regional Ocean Modeling System) runs are examined at the sea east of Sri Lanka (SESL) where intense upwelling occurs during summer monsoon (May to August). Upwelling enhances pCO₂ by 34 μatm, whereas decrease in surface temperature and increase in surface salinity reduce pCO₂ by 24 μatm. The estimated net effect of upwelling is an increase in pCO₂ by 10 μatm. In contrast, soft and hard tissues together contribute to a decrease in pCO₂ by 21 μatm suggesting that the biological effect dominates over upwelling, resulting in a net decrease of pCO₂ by 11 μatm in the SESL. This striking contrast between the increase in pCO₂ due to physical dynamics (upwelling) and the removal of pCO₂ due to biological processes is caused by shallow (deep) nitracline (dissolved inorganic carbon‐isoline) in the SESL.