A recent review of the Great Lakes Water Quality Agreement has concluded that while controls on phosphorus inputs to Lake Michigan achieved the desired effect in offshore waters, the nearshore region continues to suffer from elevated phosphorus levels. Failure to achieve trophic state goals in the nearshore is manifested in nuisance growth of Cladophora and attendant impacts on property owners, utilities, and the public health and welfare. This study focuses on a site in Lake Michigan near Milwaukee, Wisconsin, where nuisance growth of Cladophora and associated beach fouling occur regularly. A mechanistic model simulating Cladophora growth, suitable for guiding nutrient management in the Great Lakes nearshore, is presented. The model represents an update of the Canale and Auer framework, reflecting current understandings of Cladophora ecology and offering a user-friendly interface making the software more widely available to decision makers. This Great Lakes Cladophora Model (GLCM) is first validated for the Auer/Canale data set collected in 1979 at a site on Lake Huron and then for a data set developed in 2006 for a site on Lake Michigan. Model performance under the strikingly different forcing conditions (depth, light, phosphorus levels) characteristic of these two sites affirms the widespread applicability of the tool. The GLCM is then extended to examine the impacts of ecosystem perturbation (dreissenid colonization) on Cladophora growth and to future approaches to monitoring and management.