Freshwater ecosystems play a major role in global carbon cycling through the breakdown of organic material and release of greenhouse gases (GHGs). Carbon dioxide (CO2) and methane (CH4) emissions from lakes, wetlands, reservoirs and small natural ponds have been well studied, however, the GHG emissions of highly abundant, small‐scale (<0.01 km2) agricultural dams (small stream and run‐off impoundments) are still unknown. Here, we measured the diffusive CO2 and CH4 flux of 77 small agricultural dams within south‐east Australia. The GHG emissions from these waterbodies, which are currently unaccounted for in GHG inventories, amounted to 11.12 ± 2.59 g CO2‐equivalent m2/day, a value 3.43 times higher than temperate reservoir emissions. Upscaling these results to the entire state of Victoria, Australia, resulted in a farm dam CO2‐equivalent/day emission rate of 4,853 tons, 3.1 times higher than state‐wide reservoir emissions in spite of farm dams covering only 0.94 times the comparative area. We also show that CO2 and CH4 emission rates were both significantly positively correlated with dissolved nitrate concentrations, and significantly higher in livestock rearing farm dams when compared to cropping farm dams. The results from this study demonstrate that small agricultural farm dams can be a major source of greenhouse gas emissions, thereby justifying their inclusion in global carbon budgets.