Reverse osmosis (RO) membranes have been widely applied in seawater desalination (SWRO) and wastewater reclamation as the main desalination technology since 2000. SWRO plants face challenges to reduce energy consumption and brine disposal to lessen marine pollution. To tackle these challenges, a SWRO-PRO (Pressure Retarded Osmosis) System was proposed in the “Mega-ton Water System” project under the Japanese national project of the “Funding Program for World-Leading Innovative R&D on Science and Technology” (FIRST Program). To reduce the energy consumption of the main SWRO plant, an innovative low-pressure SWRO membrane and a next generation energy recovery device (ERD) were developed by the “Mega-ton Water System” project. In addition to this research and development, a new membrane process has been proposed and confirmed as a low-pressure multi-stage SWRO (LMS). A brine conversion two-stage SWRO system was invented 20 years ago, and has been in operation for over 15 years. Application of the SWRO membrane process to actual commercial plants was an important research theme. The low-pressure multi-stage SWRO System (LMS) was an innovative method of introducing a low-pressure membrane and the membrane element in the pressure vessel was designed to avoid heavy fouling of lead elements. As a result of these developments at mega-ton scale SWRO plants, a 20% energy reduction was possible in the SWRO system of the “Mega-ton Water System”. In the development of the PRO process, a PRO hollow fiber membrane module with a maximum 13.3 w/m2 of membrane power density using a 10-inch module was established at a prototype PRO plant. Thus, a 30% energy reduction was possible using the SWRO-PRO System in the “Mega-ton Water System” at mega-ton scale SWRO plants. The brine disposal problem was also solved by this system.