Zebra mussels, Dreissena polymorpha, invaded Green Bay, Lake Michigan in the early 1990s. In 1986, prior to zebra mussel invasion, the Green Bay Metropolitan Sewerage District initiated a long-term water quality monitoring program involving 12 stations in three distinct zones along a trophic gradient in lower Green Bay. We analyzed this data set pre and post invasion using various regression models to determine the impacts of the zebra mussel on water clarity, nutrient concentrations, and the relationship between chlorophyll and phosphorus in this system. Following zebra mussel invasion, Secchi depths did not change in all three zones. Chlorophyll a concentrations decreased post zebra mussels in all zones. These differences were attributed to the filter feeding abilities of zebra mussels. Lower Green Bay exhibits a strong trophic gradient and zebra mussel impacts on the chlorophyll-phosphorus relationship differed between the three zones. We saw no changes in the chlorophyll-phosphorus relationship in zone 1, zone 2 appeared to be a transition zone with slight changes in the chlorophyll-phosphorus relationship, and in zone 3 there was evidence of an altered chlorophyll-phosphorus relationship post zebra mussels. These results indicate that the impact of zebra mussels on water quality parameters and on chlorophyll-phosphorus dynamics may differ depending on initial trophic status and on zebra mussel densities.