The estuaries provide the key pathway for travelling carbon across the land-ocean interfaces and behave as both source and sink of greenhouse gases (GHGs) in water-atmosphere systems. The sink-source characteristics of estuaries for GHGs vary spatially. The primary driving factors are adjacent ecologies (agriculture, aquaculture, etc.) and proximities to the sea. To study the sink-source characteristics of estuaries for GHGs (methane (CH4), nitrous oxide (N2O) and carbon dioxide (CO2)), the water samples were collected from 53 different locations in the estuaries for estimation of dissolved GHGs concentration and air-water GHGs exchanges. The locations represent five zones (Zone I, II, III, IV and V) based on the type and degradation status of mangroves (degraded and undisturbed), anthropogenic activities, and distance from the sea. Zone I, III, V represents to the degraded mangroves far from sea, whereas, Zone II, IV surrounded by undisturbed mangroves and nearer to sea. The average dissolved CH4 concentrations were higher in the estuaries which were adjacent to degraded mangroves (154.4 nmol L−1) than undisturbed mangroves (81.7 nmol L−1). Further, the average dissolved N2O concentrations were 48% higher in the estuaries nearer to degraded mangroves than that of undisturbed ones. Among the degraded mangrove sites, the dissolved CO2 concentrations were higher at Zone I (30.1 μmol L−1) followed by Zone III and IV, whereas in undisturbed sites, it was higher in Zone IV (22.3 μmol L−1) than Zone II (17.6 μmol L−1). Among the 53 locations, 36, 51 and 33 locations acted as a sink (negative value of exchanges) for CH4, N2O and CO2, respectively. The higher sink potential for CH4 was recorded to those estuaries adjacent to undisturbed mangroves (−791.69 μmol m−2 d−1) than the degraded ones (−23.18 μmol m−2 d−1). Similarly, the average air-water N2O and CO2 exchanges were more negative in the estuaries which were nearer to undisturbed mangroves indicating higher sink potential. The pH, and salinity of the estuary water were negatively correlated with air-water CH4 and N2O exchanges, whereas those were positively correlated with CO2 exchanges. Significantly lower dissolved GHGs and air-water GHGs exchange was observed in the estuaries adjacent to the undisturbed mangrove as compared to the degraded mangrove. The reason behind higher sink behaviours of estuaries nearer to undisturbed mangroves are higher intrusion of seawater, less nutrient availability, higher salinity, low carbon contents and alkaline pH compared to estuaries adjacent to degraded mangroves and far from sea.