Maintaining well-balanced fish populations which produce harvestable surpluses for sport and commercial fisheries and restoring a self sustaining lake trout population in Lake Ontario remains a high priority of the U.S. Fish and Wildlife Service, the New York Department of Environmental Conservation, and the Ontario Ministry of Natural Resources. The USGS Great Lakes Science Center and New York Department of Environmental Conservation (NYDEC) began annual, cooperative surveys of prey fishes in 1978 to aid in management decisions. Data collected on surveys allowed researchers to track annual changes in prey fish abundance, determine individual growth rates and define stock-recruit relations, investigate the effect of changes in prey fish populations on food habits and growth of piscivores, determine the diet of prey fishes, and investigate the effect of alewife planktivory on the zooplankton community. Simple population models of principal prey fishes and their predators were incorporated into simulation models of the Lake Ontario fish community in the early 1990s. Continuing assessment of prey fishes will provide the feedback needed by managers to assess the effect of stocking practices. Research could identify the effect of colonizing exotic fishes on established food webs and suggest management actions to deal with the invaders.