The concept of cleaner production and zero waste industrial ecosystems has been a common goal of recent industrial development for the protection of the environment. The idea is also practiced by Taipower committing himself to make fewer pollution when produces electricity. Taipower has developed the microalgae cultivation technique for greenhouse gases-carbon dioxide reduction from 2004. The applications of harvested microalgae were also studied. It attracted much attention when the study results were presented in 2008. However, the water used in microalgae cultivation was the waste cooling water. The other application of waste cooling water is to be the raw water of seawater desalination system in the power plant. To increase the reuse rate of the wasted cooling water and improve the raw water quality (a purpose of boron remove) of the seawater desalination plant, application of microalgae cultivation to be the pretreatment system for desalination was assessed. First, the water qualities of microalgae cultivation and desalination system was investigated, including the wasted cooling water, permeate of 3 μm membrane ecological ponds and ultra-filtration, and wastewater of microalgae tank. Then permeate flux and water quality of RO membrane was evaluated with different feed, i.e. the four water stream mentioned above. Characteristics of RO foulants were also determined. Finally, several mixed feed tests of the microalgae cultivation wastewater with the others were performed. The major goal of the plan is to assess the feasibility of microalgae cultivation as the pre-treatment unit of desalination system.