This paper considers the performance output tracking for a boundary controlled Direct Contact Membrane Distillation (DCMD) system. First, the mathematical properties of a recently developed mathematical model of the DCMD system are discussed. This model consists of parabolic equations coupled at the boundary. Then, the existence and uniqueness of the solutions are analyzed, using the theory of operators. Some regularity results of the solution are also established. A particular case showing the diagonal property of the principal operator is studied. Then, based on one-side feedback law the control problem, which consists of tracking both the feed and permeate outlet temperatures of the membrane distillation system is formulated. A servomechanism and an output feedback controller are proposed to solve the control problem. In addition, an extended state observer aimed at estimating both the system state and disturbance, based on the temperature measurements of the inlet is proposed. Thus, by some regularity for the reference signal and when the disturbance vanishes, we prove the exponential decay of the output tracking error. Moreover, we show the performance of the control strategy in presence of the flux noise.