This report documents the quality assurance process for the development and application of Lake Michigan Mass Balance models. The scope includes the overall modeling framework as well as the specific submodels that are linked to form a comprehensive synthesis of physical, chemical, and biological processes of Lake Michigan.. The models cited in this report include hydrodynamic, sediment transport, eutrophication, transport chemical fate, and food chain bioaccumulation. In addition, the report includes the quality assurance (QA) process for the development of atmospheric models used to describe the emission of atrazine from the agricultural portion of the watershed and its transport and deposition to the lake. It also includes the QA process for the estimation of tributary and atmospheric loads for atrazine, polychlorinated biphenyls (PCBs), trans-nonachlor (TNC), and mercury.