The Cooperative Science and Monitoring Initiative aims to generate data and information to support environmental management in the Laurentian Great Lakes of North America. On a rotating basis, efforts are focused on each lake every five years. In this study, we developed a state-of-the-art hydrodynamic and ecological modeling framework to aggregate data collected during these initiative years and from other sources, and to simulate lake eutrophication processes in Lake Ontario, with an emphasis on nearshore conditions. Model calibration and validation were based primarily on data from three initiative years (2008, 2013, and 2018). This integrated model provides a framework for data organization, understanding complex lake process interactions, and guiding future data collection. It is designed as a management support tool that can simulate lake responses to changes in loading conditions, such as sensitivity of nearshore water quality to Niagara River phosphorus loads. Its designated aim is to support evaluation of management questions in Lake Ontario by providing quantitative evaluation of the relative benefits of potential nutrient loading abatement strategies to mitigate eutrophication in the nearshore. This framework is also well suited for possible future expansion to address management issues on a whole-lake basis.