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Inland waters are hotspots of greenhouse gas (GHG) cycling, with small water bodies particularly active in the production and consumption of carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O). However, wetland ponds are being replaced rapidly by small constructed reservoirs in agricultural regions, yet it is unclear whether these two water body types exhibit similar physical, chemical, and environmental controls of GHG content and fluxes. Here, we compared the content and regulatory mechanisms of all three major GHGs in 20 pairs of natural wetland ponds and constructed reservoirs in Canada's largest agricultural region. Carbon dioxide content was associated primarily with metabolic indicators in both water body types; however, primary production was paramount in reservoirs, and heterotrophic metabolism a stronger correlate in wetland ponds. Methane concentrations were correlated positively with eutrophication of the reservoirs alone, 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 being a significantly stronger and more widespread N2O sink. Varying regulatory processes are attributed to differences in age, depth, morphology, and water‐column circulation between water body types. These results suggest that natural and constructed water bodies should be modeled separately in regional GHG budgets. Plain Language Summary: Small inland water bodies, ponds and reservoirs, are hotspots of greenhouse gas (GHG) production. However, modern farming practices replace natural wetlands by artificial reservoirs, without consideration on the effects on landscape GHG fluxes. Here we measured concentrations and controls of carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O) in locally‐paired wetland ponds and agricultural reservoirs and found that while GHG concentrations were similar in the two waterbody types, underlying mechanisms differed, owing to the differences in shape, depth, and age of individual water bodies. Shallower wetland ponds were typically more fully mixed, exhibited more oxygen at depth, and had higher nutrients and organic carbon concentrations reflecting their ages. Findings suggest that the balance between wetland drainage and reservoir construction may have a pronounced effect on regional budgets of GHG fluxes, particularly in the face of forthcoming climate changes. Key Points: CO2 content was associated with metabolism; primary production in reservoirs, but bacterial respiration in wetlandsCH4 concentrations were correlated positively with either eutrophication (reservoirs) or competitive inhibition of methanogenesis (both)N2O undersaturation was ubiquitous, but wetlands were stronger and more widespread N2O sinks [ABSTRACT FROM AUTHOR]

First‐order streams flowing through peatlands receive, carry and transform large amounts of organic carbon, methane (CH4) and carbon dioxide (CO2) but remain poorly documented. The objectives of this study were to (a) identify the origins of CO2 and CH4 (thereafter C‐GHG for carbon greenhouse gases) in a peatland headwater stream, (b) determine the environmental factors driving C‐GHG export and emissions, and (c) quantify C‐GHG losses from this system and discuss its implications. Data were collected from eight sampling sites along a 3 km boreal peatland headwater stream (Eastern Canada) over the growing seasons 2019 and 2020. The studied stream was oversaturated in pCO2 [min: 2,044; max: 23,306 μatm] and pCH4 [14; 17,614 μatm]. A mass balance model showed that ∼81% of in‐stream CO2 originated from porewater seepage while the remaining 17% and 2% originated from in‐stream productivity and methane oxidation, respectively. Porewater seepage was concluded to be the primary source of CH4. Seasonal dissolved C‐GHG concentrations were negatively correlated with the peatland water table depth, suggesting an active release of carbon‐rich peat porewater during the base flow. Nevertheless, greater C‐GHG losses occurred during stormflow periods which acted as pulses with most of the C‐GHG being shunted downstream. The sum of C‐GHG export and emissions at our site was 8.08 gC m−2 y−1 with 86% being released to the atmosphere and 14% being exported downstream. Our study demonstrates that peatland headwater streams act as large sources of C‐GHG and that precipitation events and topography control the magnitude of the fluxes. Plain Language Summary: Headwater streams are the inceptive fragment of the river network where a substantial quantity of organic carbon is released from the surrounding substrate. This terrestrial organic carbon can also be transformed into greenhouse gases (GHGs) such as methane and carbon dioxide. In the stream, those GHG can be either consumed, emitted to the atmosphere, or exported downstream. However, the respective contribution of those pathways is unknown. We sampled a stream draining a rain‐fed peatland in Eastern Canada to describe and quantify its carbon GHG dynamics. We found higher concentrations in this stream than in most headwater streams but the total carbon emissions and export were comparable. Peatland streams typically have a low velocity and gentle slope which minimizes atmospheric gas release. We also found that concentrations were greater during the low flow period, potentially because carbon‐rich porewater was released from the peat. However, greater export was reported during the few days of intense rain. The significance of this work is that GHG in headwater streams are spatially and temporally variable and controlled by the surrounding ecosystems, the intensity of rain events and the stream morphology. The inclusion of this variability will improve regional and global carbon budget estimates. Key Points: Porewater seepage accounted for 81% of the carbon dioxide (CO2) present in the stream, in‐stream production and methane (CH4) oxidation contributed to 17% and 2%86.5% of the dissolved CO2 and CH4 was emitted to the atmosphere rather than exported downstream due to gases oversaturation and slow flow46% of the CO2 and CH4 exported downstream occurred during the 10% period when water discharge rates were maximum, suggesting a pulse effect [ABSTRACT FROM AUTHOR]