The exchange of CO₂ between the air–water interfaces of estuaries is crucial from the perspective of the global carbon cycle and climate change feedback. In this regard, we evaluated the air–water CO₂ exchanges in two major estuaries—the Mahanadi estuary (ME) and the Dhamra estuary (DE) in the northern part of the Bay of Bengal, India. Biogeochemical properties of these estuarine waters were quantified in three distinct seasons, namely, pre-monsoon (March to May), monsoon (June to October), and post-monsoon (November to February). The significant properties of water, such as the water temperature, pH, salinity, nutrients, dissolved oxygen, chlorophyll-a (chl a), and photosynthetic pigment fluorescence of phytoplankton, were estimated and correlated with CO₂ fluxes. We found that the ME acted as a source of CO₂ fluxes in the monsoon and post-monsoon, while DE acted as a sink during the monsoon. The stepwise regression model showed that the fluxes were primarily driven by water temperature, pH, and salinity, and they correlated well with the phytoplankton characteristics. The chl a content, fluorescence yield, and phycobilisomes-to-photosystem II fluorescence ratios were major drivers of the fluxes. Therefore, for predicting air–water CO₂ exchanges precisely in a large area over a seasonal and annual scale in the estuaries of the Bay of Bengal, India, critical key parameters such as water temperature, pH, salinity, chl a, and fluorescence yield of phytoplankton should be taken into consideration. However, the responses of phytoplankton, both in terms of production and CO₂ capture, are critical research areas for a better understanding of air–water CO₂ exchanges in coastal ecology under climate change scenarios.