The advent of computer-based modeling tools has greatly improved the ease with which biological process modeling can be implemented. However, the calibration of a site-specific model does not always receive the same level of scrutiny as does model development, which can be detrimental to process design. For example, lack of solids mass balance closure can lead to erroneous estimates of solids retention times. Incomplete specification of nitrogen species and COD partitioning can hinder process design of nutrient removal facilities with stringent discharge criteria. These types of problems are explored in two examples of simulator calibration oat full-scale activated sludge treatment plants.