Past design of secondary clarifiers has relied on empirical experience, e.g., maximum allowable overflow rates and solids loadings. Although recent development of solids flux theory has led to increased understanding and better designs, current techniques still, by necessity, treat the clarifier and associated biological reactors in isolation, with no assurance the assumptions made for one (the selected MLSS concentration for example) are consistent with the behavior of other (e.g., the ability of the clarifier to produce an acceptable effluent quality under the design loading conditions). A state-of-the-art numerical model coupling the hydrodynamic and solids transport equations in the clarifier together with the biological and physical processes in the reactor was developed. This coupled model was used to optimize the depth of new clarifiers for the Utoy Creek Wastewater Reclamation Center in Atlanta, Georgia, given a wet weather hygrograph, variable organic loadings, and variable solids settling characteristics. The model shows that increased clarifier depth will improve effluent suspended solids concentrations at high solids loading and lower solids settling properties, and can be traded off against a larger reactor or larger clarifier diameter.