The present study focused on understanding differences in the post-monsoon carbon (C) biogeochemistry of two adjacent estuaries undergoing different levels of anthropogenic stresses by investigating anthropogenically influenced Hooghly estuary and mangrove-dominated estuaries of the Sundarbans in the north-eastern India. The salinity of well-oxygenated estuaries of the Sundarbans (DO: 91 %–104 %) varied over a narrow range (12.74–16.69) relative to the Hooghly estuary (0.04–10.37). A mixing model suggested a combination of processes including freshwater intrusion, carbonate precipitation and carbonate dissolution to be a major factor controlling dissolved inorganic C (DIC) dynamics in the freshwater regime of the Hooghly, whereas phytoplankton productivity and CO2 outgassing dominated in the mixing regime. In the Sundarbans, the removal of DIC (via CO2 outgassing, phytoplankton uptake and export to the adjoining continental shelf region) dominated its addition through mineralization of mangrove-derived organic C. The concentration of dissolved organic C (DOC) in the Hooghly was ∼40 % higher than in the Sundarbans, which was largely due to the cumulative effect of anthropogenic inputs, DOC–POC interconversion and groundwater contribution rather than freshwater-mediated input. The measured δ13CPOC in the Hooghly suggested particulate organic matter contributions from different sources (freshwater runoff, terrestrial C3 plants and anthropogenic discharge), whereas the contribution from C3 plants was dominant at the Sundarbans. The significant departure of δ13CPOC from typical mangrove δ13C in the mangrove-dominated Sundarbans suggested significant particulate organic C (POC) modification due to degradation by respiration. The average pCO2 in the Hooghly was higher by ∼1291 µatm compared to the Sundarbans with surface runoff and organic matter degradation by respiration as dominant factors controlling pCO2 in the Hooghly and Sundarbans, respectively. The entire Hooghly–Sundarbans system acted as a source of CO2 to the regional atmosphere with ∼17 times higher emission from the Hooghly compared to the Sundarbans. Taken together, the cycling of C in estuaries with different levels of anthropogenic influences is evidently different, with significantly higher CO2 emission from the anthropogenically influenced estuary than the mangrove-dominated ones.