In arid environments, water shortages due to over-allocation of river flow are often compensated by lift irrigation or pumping groundwater. In such environments, farmers using pumped irrigation can deploy on-farm energy-efficient and water-saving technologies; however, pumping water requiring extra energy is associated with carbon emissions. This study explores how to increase crop production using pumped irrigation with minimal energy and carbon emissions. The purpose of this research is twofold: first, to examine on-farm energy consumption and carbon emissions in gravity and groundwater irrigation systems; and second, to explore system-level alternatives of power generation and water management for food production based on the results from the farm-level analysis. This study employs a novel system-level approach for addressing water, energy, and carbon tradeoffs under pumped irrigation using groundwater. These tradeoffs are assessed at farm and system levels. On-farm level estimates showed that farm-level interventions were insufficient to produce mutual gains. According to the results of the system-level evaluation, system-level interventions for water and energy conservation, the use of renewable energy to pump water for irrigation, and river basin scale cooperation are all required to maintain crop production while reducing energy consumption and carbon emissions.