The loss and degradation of mangroves can result in potentially significant sources of atmospheric greenhouse gas (GHG) emissions. For mangrove rehabilitation carbon projects, quantifying GHG emissions as forests regenerate is a key accounting requirement. The current study is one of the first attempts to systematically quantify emissions of carbon dioxide (CO2), nitrous oxide (N2O) and methane (CH4) from: 1) aquaculture ponds, 2) rehabilitating mangroves, and 3) intact mangrove sites and frame GHG flux within the context of landuse change. In-situ static chamber measurements were made at three contrasting locations in Sulawesi, Indonesia. The influence of key biophysical variables known to affect GHG flux was also assessed. Peak GHG flux was observed at rehabilitating (32.8 ± 2.1 Mg CO2e ha-1 y-1) and intact, mature reference sites (43.8 ± 4.5 Mg CO2e ha-1 y-1) and a dry, exposed disused aquaculture pond (30.6 ± 1.9 Mg CO2e ha-1 y-1). Emissions were negligible at low productivity rehabilitating sites with high hydroperiod (mean 1.0 ± 0.1 Mg CO2e ha-1 y-1) and an impounded, operational aquaculture pond (1.1 ± 0.2 Mg CO2e ha-1 y-1). Heterogeneity in biophysical conditions and geomorphic position exerted a strong influence on GHG flux, with the longer hydroperiod and higher soil moisture content of seaward fringing mangroves correlated with decreased fluxes. A greater abundance of Mud lobster mounds and root structures in landward mangroves correlated to higher flux. When viewed across a landuse change continuum, our results suggest that the initial conversion of mangroves to aquaculture ponds releases extremely high rates of GHGs. Furthermore, the re-institution of hydrological regimes in dry, disused aquaculture ponds to facilitate tidal flushing is instrumental in rapidly mediating GHG flux, leading to a significant reduction in baseline emissions. This is an important consideration for forest carbon project proponents seeking to maximise creditable GHG emissions reductions and removals.