The process of thermal seawater desalination depends on the heat transfer efficiency and mechanisms of scale formation on the heating surface. These processes are characterized by considerable complications and physical appropriateness describing them as not subject to get for other working mediums. Not enough attention is paid to the peculiarities of these procesess, since most investigations on desalination plants analyze their thermal scheme and elements (evaporator, heater, compressor, etc.). Seawater is a multi-component solution and its behaviour in the process of thermal desalination is not subject to those appropriatenesses which are taken to thermal and expenditure prices of this process. In this work we have shown that most modem experimental and theoretical models of the mechanism of scale formation do not take into consideration their connection to a heat transfer process. Using the pilot plants we have made comparative investigations in which the processes of heat transfer and scale formation are considered as an integral process. Scale formation on the heating surface is also described in the article. We have also suggested equations for calculating the heat transfer during seawater boiling taking into consideration the formation of scale. We have shown that the mechanism of scale formation in desalination plants is influenced by seawater magnetic treatment. The tests carried out on acting ship desalination plants have confirmed the results of the experimental observations.