Abstract. Biogeochemical cycling of CH₄ was studied in Sundarbans mangrove system during June 2010 to December 2012. The sediment was CH₄ supersaturated with mean production potential of 3547 and 48.88 µmol m⁻³ d⁻¹, respectively in case of intertidal (0–25 cm depth) and sub-tidal sediments (first 5 cm depth). This induces significant CH₄ out-flux from sediment to estuary via advective and diffusive transports. Mean advective (from intertidal sediment) and diffusive (from sub-tidal sediment) CH₄ fluxes were 159.52 μmol m⁻² d⁻¹ and 8.45 μmol m⁻² d⁻¹, respectively. Intertidal sediment CH₄ emission rate was about 4 times higher than surface layer CH₄ oxidation rate; indicating petite methanotrophic activity in mangrove sediment. Mean CH₄ concentration in estuarine surface and bottom waters were 69.90 and 56.17 nM, respectively. CH₄ oxidation in estuarine water column being 14 times higher than water–atmosphere exchange is considered as principal CH₄ removal mechanism in this estuary. Mean CH₄ mixing ratio over the mangrove forest atmosphere was 2.013 ppmv. The ecosystem acts a source of CH₄ to the upper atmosphere having mean biosphere–atmosphere exchange flux of 0.086 mg m⁻² d⁻¹. Mean CH₄ photo-oxidation rate in the mangrove forest atmosphere was 3.25 × 10^-9 mg cm⁻³ d⁻¹ and is considered as principal CH₄ removal mechanism in the forest atmosphere. Finally, a box model presenting CH₄ biogeochemistry in Sundarbans biosphere reserve has been drafted and was used to demonstrate CH₄ budget in this ecosystem.