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 CO 2 outgassing dominated in the mixing regime. In the Sundarbans, the removal of DIC (via CO 2 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 δ 13 CPOC in the Hooghly suggested particulate organic matter contributions from different sources (freshwater runoff, terrestrial C 3 plants and anthropogenic discharge), whereas the contribution from C 3 plants was dominant at the Sundarbans. The significant departure of δ 13 CPOC from typical mangrove δ 13 C in the mangrove-dominated Sundarbans suggested significant particulate organic C (POC) modification due to degradation by respiration. The average pCO 2 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 pCO 2 in the Hooghly and Sundarbans, respectively. The entire Hooghly- Sundarbans system acted as a source of CO 2 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 CO 2 emission from the anthropogenically influenced estuary than the mangrove-dominated ones. © Author(s) 2019.