Collaborative Lake Ontario bottom trawl surveys, led by the United States Geological Survey (USGS), provide science and management information for evaluating Fish Community Objectives including predator-prey balance and prey fish community diversity. In 2018, the New York State Department of Environmental Conservation (NYSDEC), Ontario Ministry of Natural Resources and Forestry (OMNR), and the (USGS) completed an April bottom trawl survey (n = 208 tows) and an October survey (n = 118 tows), at depths 6-228 m, and captured 384,651 fish from 31 species. Alewife were 80% of the total catch by number and round goby, deepwater sculpin, and rainbow smelt comprised 12, 4, and 3% of the catch, respectively. The adult alewife abundance index for U.S. waters decreased in 2018 relative to 2017, while the index in Canadian waters increased. While lake wide density increased, biomass indices for Age-2 alewife decreased. Alewife condition indices were below the 10-year average for both the April and October indices. The 2018 Age-1 alewife abundance index, which measures reproductive success the previous year, was the third lowest observed in U.S. waters over the past 22 years. The Canadian Age-1 index 2018 value was four-times larger than the U.S. value. Within-year differences between Canadian and U.S. alewife abundance indices, highlight the importance of assessing Lake Ontario fishes at a whole-lake scale. Abundance indices for rainbow smelt, threespine stickleback and emerald shiner were similar to 2017. New experimental trawl sites in embayment habitats generally captured more species, a higher proportion of native species, and higher densities relative to similar depth sites in the main lake and regions adjacent to embayments. Pelagic prey fish diversity continues to be low because a single species, alewife, dominates the catch. Deepwater sculpin and round goby were the most abundant demersal (bottom-oriented) prey fishes in 2018. Slimy sculpin and native nearshore demersal prey fishes, which were historically more abundant in trawl catches, are rare and restricted to specific habitats, since round goby proliferation. Despite declines in some species, demersal prey fish community diversity continues to increase as deepwater sculpin and round goby comprise more even portions of the community in contrast to when a single species, slimy sculpin, dominated the community. Five bloater were captured in the 2018 surveys which is the largest number captured in Lake Ontario since restoration stocking began in 2012.