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Water and energy are closely linked natural resources – the transportation, treatment, and distribution of water depends on low-cost energy; while power generation requires large volumes of water. Seawater desalination is a mature technology for increasing freshwater supply, but it is essentially a trade of energy for freshwater and is not a viable solution for regions where both water and energy are in short supply. This paper discusses the development and application of a renewable-energy-driven reverse osmosis (RO) system for water desalination and the treatment and reuse of aquaculture wastewater. The system consists of (1) a wind-driven pumping subsystem, (2) a pressure-driven RO membrane desalination subsystem, and (3) a solar-driven feedback control module. The results of the pilot experiments indicated that the system, operated under wind speeds of 3 m s−1 or higher, can be used for brackish water desalination by reducing the salinity of feedwater with total dissolved solids (TDS) of over 3 000 mg L−1 to product water or permeate with a TDS of 200 mg L−1 or less. Results of the pilot experiments also indicated that the system can remove up to 97% of the nitrogenous wastes from the fish pond effluent and can recover and reuse up to 56% of the freshwater supply for fish pond operation.