The authors document the status of Lake Ontario's open-water fish community in 1972, near the beginning of an era of massive fish stocking and when phosphorus levels in the lake from anthropogenic inputs, were near their peak. They then describe changes that occurred in the fish community in 1978-98. This was a period when large numbers of young salmonid piscivores were released annually, sea lamprey control continued to improve, and phosphorus levels were declining due to successful nutrient abatement programs. Coincident with the above, the lower food web was changed by the addition of new exotic invertebrates, the zooplankter Bythotrephes cederstroemi and particularly the zebra mussel, Dreissena polymorpha, and quagga mussel, D. bugensis. The picture of the fish community structure is drawn from records of catches in bottom trawls and gill nets during surveys of southern Lake Ontario conducted the the U.S. Geological Survey (USGS) and the New York Department of Environmental Conservation (NYDEC), from records of fish stocked in Lake Ontario by the NYDEC, and from a creel census of boat anglers returning to southern Lake Ontario ports conducted by the NYDEC.