In 21st century, availability of fresh water, industrial and domestic purpose water is low because of demand and supply of fresh water is changing with growing population. The problem is increasing pollution and salinity in fresh water. Nuclear desalination is the conclusion of drinking water from the sea water in the plant, in which the nuclear reactor is for energy source for desalination processing. Electrical energy and / or thermal energy may be used in the desalination process. In India, a total of 22 nuclear reactors with a total installed capacity of 6780 MW are in operation. The interest in the desalination of nuclear power is driven by the increasing demand for fresh water. Nuclear reactors are also used for non-power applications, using it for sea water desalination for production of fresh water has been drawing interest of many countries. These include nuclear reactors with desalination systems and various nuclear desalination projects. In this paper IAEA Desalination Economic Evaluation Programme (DEEP) is used to compare cost of two different desalination systems.