A finite-element density-homogeneous lake circulation model is coupled to a finite-segment water quality model for phytoplankton modeling in the embayments of lakes. This coupled model is applied to the Rochester Embayment, Lake Ontario during the nonstratification period and to Saginaw Bay, Lake Huron throughout the whole year. A relationship is developed to favorably calculate large-scale dispersion and turbulent exchange coefficients from detailed velocities calculated from the finer-scale lake circulation model around the coarser water quality segments. The utility and advantage of using a detailed lake circulation model in eutrophication analysis is indicated and a series of steady-state calculations with a circulation model is shown to be applicable for simulation of time-variable, seasonal phytoplankton variation in embayments.