Intensive, long-term sampling in the Bay of Quinte with multiple gears (i.e. gill nets, bottom trawls, trap nets and boat electrofishing) allowed examination of the fish community and major fish populations in the context of key stressors up to 2009. Excessive nutrient input and hyper-abundant non-native fish species, White Perch and Alewife, shaped the depreciated fish community of the 1970s. After implementation of phosphorus input control measures and simultaneous winter-kills of the hyper-abundant non-native fish in the late 1970s, Walleye recovered and served to restore a predator-prey balance to the fish community by the late 1980s. However, in the absence of a significant recovery of submerged aquatic vegetation (SAV) in littoral areas, off-shore species (e.g. Alewife and White Perch) still tended to dominate; even in littoral areas. Following establishment of Dreissenid Mussels in the mid-1990s, water transparency increased and SAV increased significantly in littoral areas. This pivotal event led to a shift in the fish community that included an overall decline in Walleye, an increase followed by a decrease in Yellow Perch, and dominance by centrarchids (i.e. Bluegill, Pumpkinseed, Black Crappie and Largemouth Bass) in the nearshore. Round Goby invaded in 1999, proliferated and became important in the diet of piscivores by 2003. The current species assemblage, including the piscivores, is diverse and indicative of a healthy fish community.