<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 (CO<sub>2</sub>) and methane (CH<sub>4</sub>) 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. Here, we conducted a regional scale survey (~ 235,000 km<sup>2</sup>) to measure CO<sub>2</sub> and CH<sub>4</sub> 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 CO<sub>2</sub> concentration was best estimated by a combination of internal metabolism and groundwater-derived alkalinity (65.7 % deviance explained), while multiple lines of evidence support a positive association between eutrophication and CH<sub>4</sub> production (74.1 % deviance explained). Fluxes ranged from −21 to 466 and 0.14 to 92 mmol m<sup>−2</sup> d<sup>−1</sup> for CO<sub>2</sub> and CH<sub>4</sub>, respectively, with CH<sub>4</sub> contributing an average of 74% of CO<sub>2</sub>-equivalent (CO<sub>2</sub>-e) emissions. Approximately 19 % farm reservoirs were found to be net CO<sub>2</sub>-e sinks. From our models, we show that the GHG impact of farm reservoirs can be greatly minimised through overall improvements in water quality and the construction and maintenance of deeper reservoirs.</p>