The project team constructed a conceptual model of river-based ecosystems that illustrates the relationships and response of various physical and biological components to a range of ecosystem stressors. The team identified a suite of existing quantitative models that could be linked to produce a prototype model for a specific watershed. After evaluating six Great Lakes watersheds, the project team selected the Muskegon River watershed for testing and application of the prototype model. The project team collaborated with The Nature Conservancy to implement and test the approach on the Muskegon watershed as part of the prototype modeling effort. This model could facilitate the evaluation of ecosystem changes by proposed water withdrawals for Great Lakes hydrologic systems.