A fractional-order robust controller to control a reverse osmosis desalination plant is proposed. The dynamics of this plant was experimentally identified. A multivariable mathematical model was obtained which showed large plant parameter variations. The proposed control system is composed of a decoupler, a diagonal compensator of the less variable dynamics, and a fractional order PI controller in each of the two loops. The fractional orders of these last controllers were optimized in order to improve the phase margin robustness. It was shown that these controllers outperformed the robustness achieved using PI controllers.