Carbon dioxide species were studied in Mandovi‐Zuari system, a tropical estuarine complex influenced by strong monsoonal run‐off, with implications to build up and air‐water exchange of CO2. Total carbon dioxide (TCO2) behaved conservatively during the estuarine mixing. Partial pressure of carbon dioxide (pCO2), evaluated from TCO2 and pH couple, and carbonic acid dissociation constants, exhibited supersaturation with respect to atmospheric CO2 round the year. The pCO2 attained maximal levels over 2000 µatm in waters of early estuarine mixing. Average pCO2 in estuarine system were 1045 and 1153 µatm (three times to that in atmosphere) in non‐ southwest (SW) and SW monsoon seasons, respectively. An experimental study revealed that soil‐water interaction could be an important controller of pCO2 abundance in these estuarine waters. The calculated water‐to‐air average fluxes were 67 and 11 mmol m−2 d−1, respectively, in SW monsoon due to higher wind speeds and non‐SW monsoons. This study strongly suggests that pH regulation by soil‐water interaction is important, besides biological processes, in river and estuarine systems.

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