The fugacity of CO2 (fCO2 (water)) and air‐water CO2 flux were compared between a river‐dominated anthropogenically disturbed open estuary, the Hugli, and a comparatively pristine mangrove‐dominated semiclosed marine estuary, the Matla, on the east coast of India. Annual mean salinity of the Hugli Estuary (≈7.1) was much less compared to the Matla Estuary (≈20.0). All the stations of the Hugli Estuary were highly supersaturated with CO2 (annual mean ~ 2200 µatm), whereas the Matla was marginally oversaturated (annual mean ~ 530 µatm). During the postmonsoon season, the outer station of the Matla Estuary was under saturated with respect to CO2 and acted as a sink. The annual mean CO2 emission from the Hugli Estuary (32.4 mol C m−2 yr−1) was 14 times higher than the Matla Estuary (2.3 mol C m−2 yr−1). CO2 efflux rate from the Hugli Estuary has increased drastically in the last decade, which is attributed to increased runoff from the river‐dominated estuary.

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