Many regions around the world are suffering from water stress, and desalinated water and recycled water are seen as alternatives for meeting the water demand. However, high energy consumption and associated greenhouse gas emissions are some of the main environmental impacts. This is notable for many arid and semi-arid countries where desalination and water recycling are considered options for ensuring water resources availability. This research presents the incorporation of the quantification of greenhouse gas emissions generated during the operation of desalination and wastewater treatment plants in the assessment of water stress levels using the water stress indicator adopted by the 2030 Agenda for Sustainable Development. Chile was chosen as a case study, as it is a country where there is a considerable difference between the availability of conventional water sources and the water demand, and the electrical grid is fed mainly by fossil fuels. The methodology proposed allows calculating the indirect greenhouse gas emissions due to electrical consumption for the operation of desalination and wastewater treatment plants, and the direct greenhouse gas emissions coming from biological processes used in wastewater treatment plants. The results showed that Chilean arid climate zones will not experience water stress in the future at the regional level, mainly because of the installation of several desalination plants by 2030. Meanwhile, recycled water from the urban sector will slightly contribute to the reduction in the level of water stress in almost all Chilean regions by 2030. Moreover, desalination and wastewater treatment plant will contribute only between 0.34% and 0.75% of total greenhouse gas emitted in Chile by 2030. Therefore, the operation of these industrial systems for facing water scarcity problems in northern and central zones of Chile is a suitable alternative because it does not generate large environmental problems.