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Abstract As the largest freshwater estuary in the Laurentian Great Lakes, Green Bay, Lake Michigan (USA) is an important ecosystem presenting both challenges and opportunities for investigating changes in the face of multiple anthropogenic stressors. We collected new data from 2000 to 2007 to assess changes in lower food web interactions after establishment of invasive species (Bythotrephes longimanus and Morone americana in 1988 and Dreissena polymorpha in 1993) and nutrient reductions (1990s). Phytoplankton and zooplankton biomass and composition, as well as primary productivity and zooplankton community grazing rates, were determined along the previously well-studied trophic gradient from the shallow Lower bay to the stratified, open-water Middle bay. A clear trophic gradient still occurred during 2000–2007, with higher nutrients, phytoplankton and zooplankton in Lower bay compared to Middle bay. Phytoplankton abundance and cyanobacteria dominance increased significantly compared to earlier studies. However, integrated primary productivity did not change significantly at either Lower or Middle bay. Zooplankton standing stock decreased in Lower bay, driven primarily by reductions of bosminids, chydorids, and cyclopoid copepods, but did not change in Middle bay. Zooplankton community grazing rates did not change significantly, but shifts in magnitude and seasonality of net phytoplankton growth rates are consistent with increased phytoplankton standing stocks. Changes in zooplankton composition indicate increased predation by invertebrates and decreased fish predation. Shifts in both bottom-up and top-down factors have occurred, with Lower and Middle bay regions more eutrophic and similar to each other as a result of changes in this highly productive Great Lakes embayment. [ABSTRACT FROM AUTHOR]