This paper deals with dynamical behavior and controlled system of a feed-flow-reversal in a RO desalination systern, giving inspirations to effective water treatment under large uncertainties, disturbances, and noises. The phase plane and nullclines analyses show an overview of RO nonlinear dynamical behavior around its equilibrium points. From a safety operation perspective, although the process variables still converge to a stable node under parametric variations, the desalination process becomes susceptible to external disturbances and suffers from severe damages due to the random occurrence of water hammering. In turn, the transient pressure has wave profile with maximum value, which can be worsen by CP phenomenon. For controlling purpose, a linear RO system with two inputs and three outputs is realized by the model linearization around the equilibrium points. This model has to be given in state-space parametric uncertainty framework considering the CP phenomenon. Overcoming the various challenges, the robust Hee controller has been designed to cope with large parametric variations and unmodeled dynamics uncertainties, and also to regulate the desalination plants under noises and disturbances such as water hammering. Finally, the simulated results show that the presented controller can offer for robust and safe operations of RO dynamical system. (C) 2016 Elsevier B.V. All rights reserved.