A bioassay procedure to assess habitat quality was tested on Port Austin reef in southern Lake Huron, a spawning area of lake trout Salvelinus namaycush. In 1986, Plexiglas incubators filled with fertilized lake trout eggs were buried by scuba divers in rock rubble at two sites. The incubators then were attached to chains between large trap-net anchors on the bottom and left over winter. At one site, egg hatch rate was significantly higher in incubators that remained buried in substrate (24%) than in incubators that were dislodged out onto the substrate (13%). At the other, more exposed site, no significant difference was found in percent hatch between eggs that incubated in (10%) and on (8%) the substrate. Percent hatch at both sites was significantly lower than that (40%) of eggs from the same source that were incubated in controlled laboratory conditions. In autumn, concentrations of dissolved ammonia, hydrogen sulfide, and nitrate near bottom and in the substrate posed no threat to lake trout embryos and were not correlated with hatch rate; concentrations differed significantly between the two sites. During winter, 15 cm of sediment settled from the water onto the reef but did not accumulate or smother the eggs. The bioassay procedure is easy to implement, is recommended for use in the Great Lakes, and could be adapted easily for use elsewhere.