Modeling and simulation of a complex biological process for the removal of nutrients (nitrogen and phosphorus) from municipal wastewater are addressed. The model developed in this work employs a distributed-parameter approach to describe the behavior of components within three different bioreaction zones and the behavior of sludge in a secondary settler. Results from a comprehensive experimental validation on an existing pilot-scale biological-nutrient-removal activated-sludge plant show that model prediction of the components＇ dynamics is generally good with the exception of acetate in the anaerobic zone and soluble phosphate in the aerobic zone in two experiments. Good results are achieved despite the apparent plant-model mismatch, such as uncertainties with the behavior of phosphorus-accumulating organisms. Validation of the proposed secondary-settler model shows that if is superior to two state-of-the-art models in terms of the sum of the square relative errors.