Mangrove ecosystems are recognized worldwide as extremely productive land-sea interfaces that play a major role in the cycling of carbon. However studies on their roles as sources or sinks of greenhouse gases such as carbon dioxide (CO2) and methane (CH4) remains limited. The present study reports the partial pressure of CO2 (pCO2) and dissolved CH4 concentrations in the Jharkhali region of the Sundarbans, the biggest mangrove delta in the world, are measured spatially in this study. For comparative purposes, samples were collected from a nearby anthropogenically affected coastal plain estuary, the first deltaic offshoot of the Ganges. An equilibrator–NDIR system and gas chromatography were used to measure the pCO2 and CH4 of surface water, respectively. Average pCO2 was 411 ± 39.7 μatm (range: 353–476 μatm), corresponding to ~109 % saturation, whereas dissolved CH4 concentrations averaged 13.3 ± 6.5 nmol L-1 (range: 5.8–30.9 nmol L-1), ~607 % saturated with respect to the atmosphere. Throughout the sampled transect, both gases were supersaturated with weak relationships between O2 and salinity. The predominance of heterotrophic respiration and tidal exchange in controlling gas distributions is indicated by weak correlations between pCO2, salinity, and particulate organic carbon (POC). Samples of the Hooghly estuary showed significantly higher pCO2 (930–1068 μatm) and dissolved CH4 (3.6–29.8 nmol L-1), indicating significant anthropogenic inputs and eutrophication. The contrasting trends show how tidal mechanisms, organic matter loading, and hydrodynamics may play a role in regulating greenhouse gas dynamics in tropical estuaries.