The different aspects of carbon biogeochemistry were studied during the postmonsoon at the Hooghly-Sundarbans estuarine system, a part of the Ganga-Brahmaputra river system located in the northeastern India. The study focused on understanding the differences in carbon biogeochemistry of estuaries undergoing different levels of anthropogenic stress by investigating anthropogenically influenced Hooghly estuary and mangrove-dominated estuaries of the Sundarbans. The salinity of well oxygenated (%DO: 91–104 %) estuaries of the Sundarbans varied over a narrow range (12.74–16.69) during postmonsoon relative to the Hooghly (0.04–10.37). Phytoplankton productivity and carbonate precipitation and/or dissolution were dominant processes controlling DIC dynamics in different parts of the Hooghly, whereas signal for mangrove derived DIC removal was observed in the Sundarbans. Influence of groundwater on estuarine DIC biogeochemistry was also observed in both the estuaries with relatively higher influence at the Hooghly than Sundarbans. In both estuarine systems, DOC behaved non-conservatively with ~ 40 % higher DOC level in the Hooghly compared to the Sundarbans. No significant evidence of phytoplankton production on DOC level was found in these estuaries, however signal of DOC input through pore-water exchange at the Sundarbans was observed. Relatively lower δ 13 C POC at the Hooghly compared to the Sundarbans suggest relatively higher terrestrial influence at the Hooghly with a possibility of in situ biogeochemical modifications of POC at the Sundarbans. The freshwater run-off coupled with in situ aerobic OC mineralization controlled estuarine p CO 2 level at the Hooghly, whereas the same was principally exogenous for the Sundarbans. The entire Hooghly-Sundarbans system acted as source of CO 2 to the regional atmosphere with ~ 17 times higher emission from the Hooghly compared to Sundarbans. The present study clearly establishes the dominance of anthropogenically influenced estuary over relatively pristine mangrove dominated one in the regional greenhouse gas budget and climate change perspective.