Geothermal waters are a source of clean energy. They should be used in a rational manner especially in energy and economic terms. Key factors that determine the conditions in which geothermal waters are used, the amount of energy obtained and the manner in which cooled water is utilised include water salinity. Elevated salinity levels and the presence of toxic microelements may often lead to difficulties related to the utilisation of spent waters. Only a few Polish geothermal facilities operate in a closed system, where the water is injected back into the formation after having been used. Open (with water dumped into surface waterways or sewerage systems) or mixed (only part of the water is re-injected into the formation via absorption wells while the rest is dumped into rivers) arrangements are more frequently used. In certain circumstances, the use of desalinated geothermal water may constitute an alternative enabling local needs for fresh water to be met (e.g. drinking water). The assessment of the feasibility of implementing the water desalination process on an industrial scale is largely dependent on the method and possibility of disposing of, or utilising, the concentrate. Due to environmental considerations, injecting the concentrate back into the formation is the preferable solution. The energy efficiency and economic analysis conducted demonstrated that the cost effectiveness of implementing the desalination process in a geothermal system on an industrial scale largely depends on the factors related to its operation, including without limitation the amount of geothermal water extracted, water salinity, the absorption parameters of the wells used to inject water back into the formation, the scale of problems related to the disposal of cooled water, local demand for drinking and household water, etc. The decrease in the pressure required to inject water into the formation as well as the reduction in the stream of the water injected are among the key cost-effectiveness factors. Ensuring favourable desalinated water sale terms (price/quantity) is also a very important consideration owing to the electrical power required to conduct the desalination process.