This paper presents the application of a model-based methodology for improved understanding of the tight interplay between effluent quality, energy use, and fugitive emissions in wastewater treatment plants. Dynamic models are developed and calibrated in an objective to predict the performance of a conventional activated sludge plant owned and operated by Sydney Water, Australia. A scenario-based approach is applied to quantify the effect of key operating variables on the effluent quality, energy use, and fugitive emissions. Operational strategies that enable a reduction in aeration energy by 10–20% or a reduction of total nitrogen discharge down to 3 mg L−1 are identified. These results are also compared to an upgraded plant with reverse osmosis in terms of energy consumption and greenhouse gas emissions. This improved understanding of the relationship between nutrient removal, energy use, and emissions will feed into discussions with environmental regulators regarding nutrient discharge licensing.