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<p>Small farm reservoirs are abundant in many agricultural regions across the globe and have the potential to be large contributing sources of carbon dioxide (<span class="inline-formula">CO₂</span>) and methane (<span class="inline-formula">CH₄</span>) to agricultural landscapes. Compared to natural ponds, these artificial waterbodies remain overlooked in both agricultural greenhouse gas (GHG) inventories and inland water global carbon (C) budgets. Improved understanding of the environmental controls of C emissions from farm reservoirs is required to address and manage their potential importance in agricultural GHG budgets. Here, we conducted a regional-scale survey (<span class="inline-formula">∼</span>&thinsp;235&thinsp;000&thinsp;km<span class="inline-formula">²</span>) to measure <span class="inline-formula">CO₂</span> and <span class="inline-formula">CH₄</span> surface concentrations and diffusive fluxes across 101 small farm reservoirs in Canada's largest agricultural area. A combination of abiotic, biotic, hydromorphologic, and landscape variables were modelled using generalized additive models (GAMs) to identify regulatory mechanisms. We found that <span class="inline-formula">CO₂</span> concentration was estimated by a combination of internal metabolism and groundwater-derived alkalinity (66.5&thinsp;% deviance explained), while multiple lines of evidence support a positive association between eutrophication and <span class="inline-formula">CH₄</span> production (74.1&thinsp;% deviance explained). Fluxes ranged from <span class="inline-formula">−21</span> to 466 and 0.14 to 92&thinsp;mmol&thinsp;m<span class="inline-formula">⁻²</span>&thinsp;d<span class="inline-formula">⁻¹</span> for <span class="inline-formula">CO₂</span> and <span class="inline-formula">CH₄</span>, respectively, with <span class="inline-formula">CH₄</span> contributing an average of 74&thinsp;% of <span class="inline-formula">CO₂</span>-equivalent (<span class="inline-formula">CO₂</span>-e) emissions based on a 100-year radiative forcing. Approximately 8&thinsp;% of farm reservoirs were found to be net <span class="inline-formula">CO₂</span>-e sinks. From our models, we show that the GHG impact of farm reservoirs can be greatly minimized with overall improvements in water quality and consideration to position and hydrology within the landscape.</p>