This data set contains Lake Trout (Salvelinus namaycush) egg catch per unit effort (CPUE) estimates obtained from egg traps set on Stony Island Reef in Lake Ontario. These data were collected from sampling efforts in November 2017 and October-November 2019. Stony Island Reef is a cobble spawning reef located in the eastern basin of Lake Ontario and was chosen as the study site because it was identified previously as an important spawning area for the extirpated native Lake Trout stock and was the focus of earlier Lake Trout reproduction studies. The two files in this data set include a comma delimited machine-readable file (*.csv) containing the Lake Trout egg trap CPUE information and an XML file containing the metadata information.