The development of an accurate biological process model of activated sludge systems is important for the control, management, and optimization of a wastewater treatment plant (WWTP). The performance of the secondary clarifier is closely related to successful operation of the WWTP, and the most suitable secondary clarifier model for activated sludge process modeling is the one-dimensional layered model. The one-dimensional layered model combined with a double-exponential settling velocity model has been extensively used for secondary clarifier modeling, but the complexity in parameter estimation has limited its application and extension to a full-scale WWTP. A parameter estimation protocol of the secondary clarifier model was developed by empirical formula estimation in combination with sensitivity analysis based on sludge volume index and routine operational parameters and employed in the secondary clarifier modeling with data from a pilot-scale test and a full-scale WWTP. Based on the sensitivity analysis results, the importance of each model parameter is assessed. The one-dimensional layered clarifier model after parameter estimation provides good predictions for the suspended solids (SS) profile, and overflow and underflow SS concentrations, in both the pilot-scale clarifier test and the full-scale WWTP.