The application of deoiling hydrocyclone systems as the downstream of three-phase gravity separator (TPGS) systems is one of the most commonly deployed produced water treatment processes in offshore oil and gas production. Due to the compact system’s complexity and tailor-made features, it is always challenging to develop some optimally coordinated control solution for the coupled hydrocyclone and TPGS systems. It is obvious that coordinated control can better fulfill legislative discharge regulation by robustly maintaining high separation efficiencies. This paper presents a new control solution for a set of integrated hydrocyclone and TPGS systems by applying an improved multi-variable model reference adaptive control (MV-MRAC) approach with the aim of achieving both asymptotic output tracking and unknown disturbance rejection. A robust MV-MRAC controller design is proposed based on a control parameterization derived from a factorization of a high-frequency gain matrix Kp=LDS as a product of three matrices, where L represents unity lower triangular, D=sign(D) represents diagonal, and S represents positive definite, and a teaching–learning-based optimization (TLBO) algorithm for optimizing the adaption rates. The developed solution is analyzed and compared with a commonly deployed PI control solution on a model that is derived from a lab-scale produced water treatment process. This simulation study demonstrates the promising potential of the proposed control solution compared with the currently deployed PI control solution.