In recent years, extreme climate conditions have resulted in uneven precipitations in Taiwan. The development of traditional water resources frequently suffers from protests of environmental groups, potential dam sites being hard-to-find, and other factors. The development of new water sources has been increasingly difficult. Sea water desalination has the advantages of a short construction time and easy expansion flexibility, making it an important alternative as a new water resource. In this study, the current proposal of Tainan's desalination plant was used as an example. Qualitative interviews and Analytic Hierarchy Process (AHP) were used to explore the environmental impact assessment (EIA) commissioner's perceptions of the impact from the development of the desalination project. The results of the qualitative interview indicate that the main concerns of the EIA commissioners are whether the development could damage the marine ecological environment and its fishery resources, which may have adverse socioeconomic consequences. The AHP results show that the commissioners' priority of environmental impact is ecological environmental impact 36.9%, social impact 29.7%, economic impact 23.7%, and physical and chemical environmental impact 9.7%. The main concerns in each impact category are, respectively, marine ecological environment, land and ocean utilisation, fisheries, and air quality.