This paper presents the design of a plant-wide CNP (carbon-nitrogen-phosphorus) simulation model of a full-scale wastewater treatment plant, which will be upgraded for tertiary treatment to achieve compliance with effluent total nitrogen (TN) and total phosphorus (TP) limit values. The plant-wide model of the existing plant was first designed and extensively validated under long-term dynamic operation. The most crucial step was a precise characterization of input wastewater that was performed by extending the plant performance indicators both to a water line and sludge line and systematically estimating identifiable wastewater characterization parameters from plant-wide performance indicators, i.e. effluent concentrations, biogas and sludge production, and sludge composition. The thus constructed simulation model with standard activated sludge model (ASM2d) and anaerobic digestion model (MantisAD) overpredicted ortho-P and ammonia-N on the sludge line, indicating a need to integrate state-of-the-art physico-chemical minerals precipitation models to simulate plant-wide interactions more precisely. The upgraded plant with multimode anaerobic/anoxic/oxic configuration shows limited denitrification potential. Therefore, additional reject water treatment was evaluated to improve effluent TN and TP performance.