Nowadays, water demand and water scarcity are very urgent issues due to population growth, drought and poor water quality all over the world. Therefore, water treatment plants are playing a vital role for good living condition of human. Water area needs more concentration study to increase water productivity and decrease water cost. This dissertation presents the analysis and control of water treatment plants using robust control techniques. The applied control algorithms include H∞, gain scheduled and observer-based loop-shaping control technique. They are modern control algorithms and very powerful in robust controlling of systems with uncertainties and disturbances. The water treatment plants include a desalination system and a wastewater process. Since fresh water scarcity is getting more serious, the desalination plants are to produce drinking water and wastewater treatment plants give the reusable water. The desalination system is a RO one used to produce drinking water from seawater and brackish water. The nonlinear behaviors of this system is carefully analyzed before the linearization. Due to the uncertainty caused by concentration polarization, the system is linearized using linear state-space parametric uncertainty framework. The system also suffer from many disturbances which water hammer is one of the most influential one. The mixed robust H∞ and μ-synthesis control algorithm is applied to control the RO system coping with large uncertainties, disturbances and noises. The wastewater treatment process is an activated sludge process. This biological process use microorganisms to convert organic and certain inorganic matter from wastewater into cell mass. The process is very complex with many coupled biological and chemical reactions. Due to the large variation in the influent flow, the system is modelized and linearized as a linear parametric varying system using affine parameter-dependent representation. Since the influent flow is quickly variable and easily to be measured, the robust gain scheduled robust controller is applied to deal with the large uncertainty caused by the scheduled parameter. This control algorithm often gives better performances than those of general robust H∞ one. In the wastewater treatment plant, there exist an anaerobic digestion, which is controlled by the observer-based loop-shaping algorithm. The simulations show that all the controllers can effectively deal with large uncertainties, disturbances and noises in water treatment plants. They help improve the system performances and safeties, save energy and reduce product water costs. The studies contribute some potential control approaches for water treatment plants, which is currently a very active research area in the world.