The paper presents an attempt to assess sustainability of desalination plants for water production based on resource, environmental and economic indicators. Four types of desalination plants are taken into a consideration: single MSF, dual purpose MSF, RO with local energy consumption and RO with PV electric energy production. The analysis is based on data from desalination plants in Gulf countries. In particular, it reflects water production demand and energy sources used for the individual plants. The decision-making procedure in the sustainability assessment of desalination plants is based on the multi-criteria evaluation under uncertainty of complex systems expressed by the General Sustainability Index. Evaluation of different cases reflecting priority of the criteria for evaluation has led to the selection of options, which are in compliance with respective criteria.