Inland waters are hotspots of greenhouse gas (GHG) emissions, and small water bodies are now well known to be particularly active in the production and consumption of carbon dioxide (CO₂), methane (CH₄), and nitrous oxide (N₂O). High variability in physical, chemical, and environmental parameters affect the production of these GHG, but currently the mechanistic underpinnings are unclear, leading to high uncertainty in scaling up these fluxes. Here, we compare the relative magnitudes and controls of emissions of all three major GHG in twenty pairs of natural wetland ponds and constructed reservoirs in Canada’s largest agricultural region. While gaseous fluxes of CO₂ and CH₄ were comparable between the two waterbody types, CH₄ ebullition was greater in wetland ponds. Carbon dioxide levels were associated primarily with metabolic indicators in both water body types, with primary productivity paramount in agricultural reservoirs, and heterotrophic metabolism a stronger correlate in wetland ponds. Methane emissions were positively driven by eutrophication in the reservoirs, while competitive inhibition by sulfur-reducing bacteria may have limited CH₄ in both waterbody types. Contrary to expectations, N₂O was undersaturated in both water body types, with wetlands a significantly stronger and more widespread N₂O sink than were reservoirs. These results support the need for natural and constructed water bodies for regional GHG budgets and identification of GHG processing hotspots.