Behind their role as carbon sinks, mangrove soil can also emit greenhouse gases (GHG) through microbial metabolism. GHG flux measurments of mangroves are scarce in many locations, including Indonesia, which has one of the world’s most extensive and carbon-rich mangrove forests. We measured GHG fluxes (CO2, CH4, and N2O) during the wet season in Benoa Bay, Bali, a bay with considerable anthropogenic pressures. The mangroves of this Bay are dominated by Rhizophora and Sonneratia spp and have a characteristic zonation pattern. We used closed chambers to measure GHG at the three mangrove zones within three sites. Emissions ranged from 1563.5 to 2644.7 µmol m−2 h−1 for CO2, 10.0 to 34.7 µmol m−2 h−1 for CH4, and 0.6 to 1.4 µmol m−2 h−1 for N2O. All GHG fluxes were not significantly different across zones. However, most of the GHG fluxes decreased landward to seaward. Higher soil organic carbon was associated with larger CO2 and CH4 emissions, while lower redox potential and porewater salinity were associated with larger CH4 emissions. These data suggest that soil characteristics, which are partially determined by location in the intertidal, significantly influence GHG emissions in soils of these mangroves.