Surface water partial pressure of carbon dioxide [pCO2 (water)], total alkalinity (TA), dissolved inorganic carbon (DIC), and air–water CO2 flux were measured in two estuaries of the Bay of Bengal namely Mahanadi and Dhamra. Though the annual average air–water CO2 fluxes at the Mahanadi and the Dhamra Estuaries were − 3.9 ± 21.4 (mean ± standard deviation) µmol m−2 h−1 and − 2.9 ± 11.6 µmol m−2 h−1, respectively, the intra-annual variation of air–water CO2 fluxes in the two estuaries was contrasting. Nonetheless, from the perspective of net primary productivity, the surface water of both the estuaries were found autotrophic throughout the study period with varying rates at different seasons and highest during summer months. Mahanadi Estuary acted as a CO2 source toward atmosphere during monsoon months, whereas, Dhamra Estuary acted as a source during pre-monsoon months. On the contrary, Mahanadi and Dhamra Estuaries acted as CO2 sink during pre-monsoon months and monsoon months, respectively. The salinity in Mahanadi Estuary was much lower compared to Dhamra, which indicated significant freshwater discharge rich in organic carbon, and the remineralization of this carbon to DIC during summer and monsoon months explained the CO2 source character. Whereas, in Dhamra, reduced freshwater flow and high turbidity were held accountable for net heterotrophic character of the water column during the post-monsoon months. The annual data set of air–water CO2 fluxes from these two estuaries produced from this study could be utilized in future to fill the data gap and upscale the Indian estuaries scenario from the perspective of blue carbon budgeting.