Environmental concerns include air pollution and greenhouse gas emissions from the power plants that provide electricity and/or thermal energy to the desalination plants.

Regardless of the method used, there is always a concentrated waste product consisting of everything that was removed from the created fresh water. This is sometimes referred to as brine, often disposed of in the ocean, and careful planning and design needs to ensure that this brine stream is dispersed as quickly as possible.

Marine life entrapment and impingement of the open sea intakes and brine outfalls for these systems is an environmental concern. Design improvements and extensive monitoring of existing systems have reduced the environmental impact of both.