A methodology is developed for the optimization of the operation of Reverse Osmosis (RO) desalination process. Thus, a computer model of the process is first presented, that comprises two sub models, the first for the solution diffusion process, and the second for the effects of membrane fouling. The optimal operation problem is then stated and transformed into a mathematical optimization problem, based on the minimization of the Specific Energy Consumption (SEC): a computer-based approach is then proposed, to periodically calculate a combination of the pressure difference across the membrane, and the feed water flow rates, that minimizes the SEC, and always fulfils given operational constraints. It is shown that this mathematical problem can be transformed into a standard nonlinear optimization problem, which can be solved using off-the-self software. Application of the methodology is demonstrated on the simulation of a real RO desalination plant, which demonstrates how the proposed approach makes possible to adapt the operation to variations in the plant conditions.