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Small farm reservoirs are abundant in many agricultural regions across the globe and have the potential to be large contributing sources of carbon dioxide (CO2) and methane (CH4) 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 (∼ 235 000 km2) to measure CO2 and CH4 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 CO2 concentration was estimated by a combination of internal metabolism and groundwater-derived alkalinity (66.5 % deviance explained), while multiple lines of evidence support a positive association between eutrophication and CH4 production (74.1 % deviance explained). Fluxes ranged from −21 to 466 and 0.14 to 92 mmol m−2 d−1 for CO2 and CH4, respectively, with CH4 contributing an average of 74 % of CO2-equivalent (CO2-e) emissions based on a 100-year radiative forcing. Approximately 8 % of farm reservoirs were found to be net CO2-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.