This dataset contains Lake Ontario prey fish abundance and distribution statistics, collected every year during spring and fall bottom trawl surveys. The New York State Department of Environmental Conservation and the U.S. Geological Survey have conducted annual, spring and fall bottom trawl surveys in U.S. waters of Lake Ontario since 1978. In 2015, the Ministry of Natural Resources and Forestry started contributing to this program to include survey coverage in Ontario waters. The ministry also intermittently conducts mid-water trawling during the summer months on a limited geographic area largely confined to the Eastern Basin. The survey has varied sample distribution across lake depths and jurisdictions. The south shore of Lake Ontario has well-distributed coverage of depths between 8 and 200 metres. Coverage along the north shore is less uniform due to a lack of suitable trawl sites at shallower depths.