Abstract: The benthic community structure in the Bay of Quinte, eastern Lake Ontario, was examined over a 40 year period (1967–2006). Changes in species composition were examined using clustering and ordination analysis at a shallow upper bay site (6 m) and in the deeper lower bay site (32 m). Tubificidae and Chironomidae, which dominated the upper bay, responded to phosphorus reductions between 1978 and 1991 with increased diversity, and a return of pollution sensitive species. This response accelerated in 1993, after the arrival of Dreissena. Epibenthic Amphipoda, Gastropoda and Sphaeriidae increased in the upper bay between 1986–1999, but decreased following the arrival of the Round Goby (Apollonia melanostomus). The lower bay underwent a major change after 1994, when Quagga Mussel replaced the amphipod Diporeia as the dominant organism. Since 1990, non-dreissenid biomass decreased in the lower bay but has not significantly changed in the upper bay. Ordination showed that the community in the upper bay changed over time, and remained different from the lower bay community. In the lower bay and Lake Ontario, the benthic community greatly changed to one very different from the historical community of the Great Lakes.