Irrigation pumping is a major expense of agricultural operations, especially in arid/semi-arid areas that extract large amounts of water from deep groundwater resources. Studying and improving pumping efficiencies can have direct impacts on farm net profits and on the amount of greenhouse gases (GHG) emitted from pumping plants. In this study, the overall pumping efficiency (OPE), the GHG emissions, and the costs of irrigation pumping were investigated for electric pumps extracting from the Rush Springs (RS) aquifer in central Oklahoma and the natural gas-powered pumps tapping the Ogallala (OG) aquifer in the Oklahoma Panhandle. The results showed that all electric plants and the majority of natural gas plants operated at OPE levels below achievable standard levels. The total emission from the plants in the OG region was 49% larger than that from plants in the RS region. However, the emission per unit irrigated area and unit total dynamic head of pumping was 4% smaller for the natural gas plants in the OG area. A long-term analysis conducted over the 2001–2017 period revealed that 34% and 19% reductions in energy requirements and 52% and 20% decreases in GHG emissions can be achieved if the OPE were improved to achievable standards for plants in the RS and OG regions, respectively.