Mangrove ecosystems can be both significant sources and sinks of greenhouse gases (GHGs). Understanding variability in flux and the key factors controlling emissions in these ecosystems are therefore important in the context of accounting for GHG emissions. The current study is the first to quantify GHG emissions using static chamber measurements from soils in disused aquaculture ponds, planted mangroves, and mature mangroves from the Ayeyarwady Delta, Myanmar. Soil properties, biomass and estimated net primary productivity were also assessed. Field assessments were conducted at the same sites during the middle of the dry season in February and end of the wet season in October 2019. Rates of soil CO2 efflux were among the highest yet recorded from mangrove ecosystems, with CO2 efflux from the 8 year old site reaching 86.8 ± 17 Mg CO2 ha−1 yr−1 during February, an average of 862% more than all other sites assessed during this period. In October, all sites had significant rates of soil CO2 efflux, with rates ranging from 31.9 ± 4.4 Mg CO2 ha−1 yr−1 in a disused pond to 118.9 ± 24.3 Mg CO2 ha−1 yr−1 in the 8 year old site. High soil CO2 efflux from the 8 year old site in February is most likely attributable to high rates of primary production and belowground carbon allocation. Elevated CO2 efflux from all sites during October was likely associated with the extreme 2019 South Asian monsoon season which lowered soil pore salinity and deposited new alluvium, stimulating both autotrophic and heterotrophic activity. Methane efflux increased significantly (50–400%) during the wet season from all sites with mangrove cover, although was a small overall component of soil GHG effluxes during both measurement periods. Our results highlight the critical importance of assessing GHG flux in-situ in order to quantify variability in carbon dynamics over time.