The application of mathematical models to a sediment stability study is presented, with an emphasis on using models as a component of an effort to develop, refine, and potentially validate a conceptual site model (CSM) for sediment transport at a study site. The utility of mathematical models is discussed, in which the modeling framework consists of linked hydrodynamic, sediment transport, and contaminant fate and transport models. Benefits and drawbacks of empirically based mechanistic models are presented. An approach for integrating modeling analyses into the development, refinement and validation of a CSM is provided. This approach focuses on a phased study that combines modeling and data-based analyses to test hypotheses related to the CSM and sediment stability. Uncertainty in modeling results is a primary concern in sediment stability studies, and issues related to model uncertainty are discussed. Finally, communication of modeling results to stakeholders is addressed.