This paper presents the design of a decentralized proportional-integral (PI) controller for a wastewater treatment plant (WWTP). The aeration rate and the return recycle sludge rate are manipulated inputs to the WWTP process, while substrate and biomass concentration are considered as the output variables. The study is divided into two segments: A decentralized controller is designed based on the best pairing in the first segment, and in the second segment, a decoupler is developed to reduce the interactions. Decouplers are generally used to create independent loops in the multivariable control loops. Each decoupled subsystem is converted to first order plus time delay (FOPTD) model using a system identification toolbox to design independent diagonal controllers. The numerical simulations have been performed to evaluate the effectiveness of the presented methods. Furthermore, a robustness study has also been carried out by taking into account multiplicative input and output uncertainties, and it is found that the controller designed based on minimizing the integral of absolute error (IAE) criteria shows more robust.