Although emerging desalination technologies such as hybrid technologies are required to tackle water scarcity, the impacts of their application on the environment, resources, and human health, as prominent pillars of sustainability, should be evaluated in parallel. In the present study, the environmental footprint of five desalination plants, including multi-stage flash (MSF), hybrid reverse osmosis (RO)–MSF, hybrid nanofiltration (NF)–MSF, RO, and hybrid NF–RO, in the Persian Gulf region, have been analyzed using life cycle assessment (LCA) as an effective tool for policy making and opting sustainable technologies. The comparison was based on the impacts on climate change, ozone depletion, fossil depletion, human toxicity, and marine eutrophication. The LCA results revealed the superiority of the hybrid NF–RO plant in having the lowest environmental impact, although the RO process produces more desalinated water at the same feed and input flow rates. The hybrid NF–RO system achieves 1.74 kg CO2 equivalent, 1.24 × 10−7 kg CFC-11 equivalent, 1.28 × 10−4 kg nitrogenous compounds, 0.16 kg 1,4-DB equivalent, and 0.56 kg oil equivalent in the mentioned impact indicators, which are 7.9 to 22.2% lower than the single-pass RO case. Furthermore, the sensitivity analysis showed the reliability of the results, which helps to provide an insight into the life cycle impacts of the desalination plants.