The addition of round goby to the Lake Ontario prey fish community can, because it appears to lack thiaminase, ameliorate the effects of a diet high in thiaminase-rich alewives associated with a thiamine deficiency in Lake Trout. However, the effects of round goby predation may negate such effects. We conducted studies to assess the proportion, by weight, of round gobies in the diet of contemporary Lake Ontario Lake Trout and predicted its effect on egg thiamine concentration, and early mortality syndrome (EMS) and growth retardation, two indicators of thiamine deficiency. We compared these parameters to that for the historic prey community, as well as possible future diet scenarios with progressively greater proportions of round goby (e.g. 50, 75 and 100%). To assess the combined and separate effects of the thiamine deficiency we used a modeling approach to determine the effect of EMS (70%) typical of Lake Ontario Lake Trout, growth retardation, density of Lake Trout egg (e.g. 100, 500, 1000, and 5000 eggs m−2) and round goby (e.g. 1, 9, 18, 35, 75, 150 gobies m−2), three separate durations of round goby residence on Lake Trout spawning habitat (e.g. 30, 60 and 213 days), and at either a shallow water or deepwater temperature regime. Eight years after first invading Lake Ontario, the proportion of round gobies in Lake Trout diets remains low, although the highest observed (25%) would result in significant amelioration of the thiamine deficiency from past conditions. Modeling indicated that the negative effects associated with round goby predation on eggs and fry could easily exceed any positive effects resulting from amelioration of the thiamine deficiency by a diet containing round goby. The effects of goby predation were found to be dependent on density of both Lake Trout eggs and round gobies, and while predation effects were minimally affected by temperature regime, they were highly dependent on the period of round goby residence on Lake Trout spawning habitat.