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This work proposes a two-time-scale framework for the design of a supervisory predictive control system for long-term optimal management and operation of an integrated wind-solar energy generation and reverse-osmosis (RO) water desalination system. Specifically, we design the supervisory control system via model predictive control (MPC) which coordinates the wind and solar subsystems as well as a battery bank to provide enough energy to the RO subsystem. In the supervisory MPC design, a two-time-scale property of the dynamics of the integrated system is taken advantage of to improve the computational efficiency of the control problem formulation. Furthermore, optimality considerations on system operation and energy savings are taken into account via appropriate constraints in the supervisory controller formulation. Simulations are carried out to illustrate the applicability and effectiveness of the proposed supervisory predictive control design.