These data include a field study of the sediment hardness and fish egg density (walleye [Sander vitreus] and lake whitefish [Coregonus clupeaformis]) after sediment cleaning treatments (propulsion sled or hydro-jet sled) conducted at two reef locations in Saginaw Bay, Lake Huron, during 2018 and 2019. The data includes the year, species, reef, treatment type (jet, fan, control), number of eggs, and egg density in the treatment area. Relative sediment hardness for the treatment areas assessed before and after sediment cleaning experiments is provided. Additionally, walleye eggs were collected from Brookville Reservoir, Indiana, and incubated at the aquaculture research laboratory at Purdue University (West Lafayette, Indiana) to determine the effect of sediment cover on egg hatching success rate. The incubated eggs were exposed to different sediment types and levels of sediment coverage intensity. The data contains the year, treatment, parental female length (2019 only), number of walleye hatched, and egg diameter (2019 only) collected in the laboratory study.