Data on greenhouse gas (GHG) exchange between water surfaces and the atmosphere above tropical peatland drainage canals are lacking in the literature. We quantified diffusion fluxes of CO2, CH4 and N2O between the water surface and the atmosphere for two typical reclaimed peatland sites. One site was an industrial pulp wood plantation in the Kampar Peninsula (Sumatra) and the other was an abandoned peatland area in Kalimantan (Borneo). Drainage canal fluxes were measured by using floating closed chambers during both the wet and dry seasons. Fluxes at the sites were determined across a range of conditions that were created by varying land use histories, and also by canal biotic environment and hydrological features. Gas fluxes in the canal systems were influenced by their respective surrounding peatland areas, the season, and canal management. Fluxes of all three gases were higher at the more recently reclaimed settled (undisturbed) canals of the Kampar site in comparison to the Kalimantan site. In general, the mean flux from the canals ranged from 9–16, 0.1–1.1 and 0–0.003 g m–2 d–1 for CO2, CH4 and N2O, respectively. A cumulative equivalent annual emission of these three GHGs from canals was nearly three times higher at the Kampar site (13.8 kg CO2 e m–2 y–1) than that at the Kalimantan site (4.8 kg CO2 e m–2 y–1). Mean fluxes of the three gases and the cumulative annual emission at the Kampar site were higher in the settled canals in comparison to the disturbed canals when both dry and wet season fluxes were calculated. The fluxes of CH4 and N2O especially decreased when canals had been recently cleaned (i.e. were in disturbed condition). In terms of their relative global warming potentials (GWP), CO2 was the most important of the three GHG’s both at the Kalimantan site settled canal (69% of the fluxes were attributed to CO2) and at the disturbed canals at the Kampar (82%) site, whereas CH4 dominated in settled canals at the Kampar site at 61% contribution to the total annual emission. CH4 contributed 31% to the total cumulative equivalent annual emission at the Kalimantan settled canal. N2O had only a minor role (0–2% of the cumulative fluxes) at the sites. On a unit area basis, GHG emissions from the drainage canals formed were generally higher emission sources in comparison to the surrounding peatland, and proportional contributions from the three GHG species to the total were more diverse in canals than on land.