Wastewater treatment plants (WWTPs) are highly non-linear processes that must be optimized to meet rigorous environmental water regulations. In this context, efficiency and costs are equally important terms. The ASM3bioP framework is employed in this study to enable simultaneous nitrogen and phosphorus removal using an activated sludge process model with seven-reactor configurations. The activated sludge process is the most complicated and energy-intensive phase of a WWTP. To control dissolved oxygen in aerobic reactors and nitrate levels in anoxic reactors, two robust PI controllers - a classical PI and a non-integer (fractional)-order PI - with both integer-order and fractional-order models are designed. The controllers are created and simulated with the use of a mathematical model that has been developed based on the input data. The lower level fractional controller with a fractional-order model improves both the effluent quality (EQI) and operational cost (OCI) indices significantly. For such biological WWTP, a hierarchical fuzzy logic controller is designed to adjust the dissolved oxygen in the seventh reactor (DO7) to control ammonia. The implemented supervisory layer control strategy improves effluent quality EQI while increasing OCI marginally.