Low-carbon water production technologies are indispensable for achieving sustainable development goals and mitigating global climate change. However, at present, many advanced water treatment processes lack a systematic assessment of related greenhouse gas (GHG) emissions. Thus, quantifying their life-cycle GHG emissions and proposing strategies toward carbon neutrality is urgently needed. This case study focuses on electrodialysis (ED), an electricity-driven desalination technology. To analyze the carbon footprint of ED desalination in various applications, a life cycle assessment model was developed based on industrial-scale ED processes. For seawater desalination, the carbon footprint is 59.74 kg CO2-eq/metric ton removed salt, which is one order of magnitude lower than that of high-salinity wastewater treatment and organic solvent desalination. Meanwhile, the power consumption during operation is the main hotspot of GHG emissions. Power grid decarbonization and improved waste recycling in China are projected to reduce the carbon footprint up to 92%. Meanwhile, the contribution of operation power consumption is expected to reduce from 95.83% to 77.84% for organic solvent desalination. Through sensitivity analysis, significant non-linear impacts of process variables on the carbon footprint were determined. Therefore, it is recommended to optimize the process design and operation to reduce power consumption based on the current fossil-based grid. GHG reduction for module production and disposal should also be emphasized. This method can be extended to general water treatment or other industrial technologies for carbon footprint assessment and reducing GHG emission.